Now, I started out as an aquarist, before I had crabs. I have a huge saltwater reef tank with a large mangrove/macro-algae refugium, as well as some freshwater tanks. One of the first things you learn in fish-keeping is to NEVER do a total water change. It totally destroys all the good bacterial colonies, and makes room for harmful bacteria, as well as stressing out the fish, because it is next to impossible to exactly match the previous temperature and pH and so forth. The problem is not that they can't handle a huge drop in the nitrates and toxins (THAT is a good thing for them to have), but that they can't handle the change in water pH, temperature, hardness, and bacterial makeup. It is advocated that you next to never do a change of more than 30-40%, and it is much better to do more frequent, smaller, water changes.
I propose that cleaning a crabitat is much like cleaning a fish tank. Both have the same reasons for being done, i.e. bacterial buildups, and toxin and waste accumulation. Both, when done in entirety, have the potential to stress out if not kill your more delicate animals, and both can deplete the good bacteria in the tank and make room for worse bacteria than were there already. I suggest that the two are similar, in that substrate, like water, is a good breeding ground for both beneficial and harmful bacteria; that crabs, like fish, spend a lot of time in that substance, and thus can be helped and harmed by the makeup of the medium; and that both need cleaned, because, as in all closed systems, there can accumulate in a short period a great many harmful things, from toxins to wastes to bacteria.
If we assume that cleaning a small, closed environment in which fragile pets live, and wastes and bacteria build up, is much the same from tank to 'tat, then we have some more conclusions that we can make.
In fish-keeping, it is considered a good idea to start your tank "seeded" with good bacteria. With a reef tank, this can be accomplished with "live" sand and rock, teeming with bacteria and small lifeforms. With a freshwater tank, this can be done with water from an existing tank, or, hard to find and hideously expensive, with "live" substrate for freshwater. In gardening, also, "seeding" a garden with beneficial organisms and bacteria is recommended. This is especially important when organically gardening, as you cannot rely on chemical solutions to combat negative bacteria and pests. Similarly, in a crabitat, there is no reason why the tank cannot also be seeded. Perhaps a handful of sand from a local beach or desert, or a handful of soil from your own pesticide free garden or forest. Something to introduce the live organisms and beneficial bacteria that will out-compete the harmful ones, as they will already have a foothold in the closed environment. Yes, using seed cultures from uncontrolled locales will introduce the possibility of "bad" hitch-hikers, but a)there are very few "controlled" sources for cultures, unlike with fish, and b) there are ways to mitigate the harmful things, and help propagate the positive ones, as we will discuss next.
Again, in aquaria, there comes up the issue of how to feed your good bacteria and critters while getting rid of the bad ones. The solutions are 2 part, environment and husbandry techniques.
Environment: So you have a fishtank full of micro algae. You can add a chemical control, a biological control, or a mechanical control. You can dose the tank with an anti-algal product (chemical). This isn't the best option, as some are harmful to the more delicate organisms in the tank. It would be like spraying pesticide in the 'tat to control mites. You can pick and scrub all the algae you can get to off (mechanical). This leaves the issue of the spores you didn't get, the bits you didn't see or reach, and so forth. The problem will come right back up. This is akin to picking off all the visible mites and eggs with a tweezers. The third option would be to get an algae eating fish, some snails or shrimp, and/or live plants (mangrove, macro-algae). The plants will out-compete the algae for food, the animals will eat it, any comes back up, they eat it too, and they all help process wastes produced by the other inhabitants of the tank. This is akin to getting the Hypoaspsis miles and seeding the 'tat with them. The best option all around, and the most natural option. It increases the bio-diversity of your environment, and helps to more closely mimic a natural habitat, leading to an increase in health.
In crab-keeping terms, a biological solution to some common problems is similar. Put live plants that will help process wastes and uneaten food in. Add beneficial insects, which, in addition to being an extra protein source, will help eat wastes, uneaten exo, and other detritus. Make sure you have good airflow, because humid, warm air with no circulation is a BREEDING ground for disease. Make sure you have good lighting, most harmful organisms prefer dark. The live plants will an occasional food source, hiding places, fresher air, and a more realistic 'tat, as well as provide your "canary in a coal mine" for bacterial buildups and toxin issues, and the insects will keep the substrate aerated, consume harmful toxins and bacteria, and help keep the 'tat nice and clean. Tree snails will also provide shells when they die

Husbandry: The hard part of the equation. In fishkeeping, this means regular small water changes, not over-feeding, removal of debris, occasional manual removal if problem organism populations get too high. As far as crabs go, it's pretty much the same. Remove uneaten food from the substrate. If you like to let stuff get good and stinky in the dish, that's fine. Clean the substrate around it, don't let it get in there and mold. No rotting food to live in=less bad bacteria in the 'tat. Remove any bad bugs or mold you see. Instead of changing out the whole tank every few months, consider removing it a bit at a time. That can be done without removing crabs. Area under the food dish looking mucky? Remove that chunk of substrate this week. The whole chunk, down to the bottom, and replace it with fresh. Mix the fresh in!!!! Everybody up?? Replace the top layer of substrate (inch or so) and again, mix it well. One of your crabs come up from molting? Take the chunk of substrate he molted in out this week. Again, replace with fresh, and mix well. Aerate the soil EVERY week, just like compost, to distribute beneficial bacterial growth throughout the medium, and expose new sections to sunlight to get rid of the bad bacteria. Replace about 10-20% of your total substrate every week. Boil or bake a few of their toys and hides each week. Clean your shells. Clean your dishes. This method is a LOT more work, but a lot less stress on your crabs (and the insects and plants you have with them). You never have to take everybody out and put them back in a "sterile" environment that VERY quickly turns into a bad-bacteria-and-bug-fest.
Just as people on antibiotics get secondary infections (like yeast infections in women), just like anything that de-populates "good" gut bacteria leads to an upsurge in the bad ones, removing the good bacteria breeding in your closed environment leads to a problematic increase in bad bacteria. A rah of bacterial infections, mold, and other issues can result. Just as doing a massive water change kills fish from the shock and stress, doing a "deep clean" puts your crabs into temporary PPS. You take them from a good environment, put them in a less than optimal one for a few hours, and then put them back in a tank that is all new, good bacteria free, waste product that they like to eat free, and expect them to be happy. Yes, in a closed environment, waste and bad bacterial counts can quickly go through the roof. However, by utilizing good husbandry techniques, and adding beneficial organisms, we can regulate our systems to the point which a total "do-over" is never necessary, rather, constant preventive and occasionally reactive maintenance will be sufficient to combat any issues. With use of live plants, you can control levels of nutrients in the substrate that allow for bacterial growth, as well as have a gauge for when things are going bad and more strenuous measures need to be taken. With use of a "seed culture" of beneficial bacteria and organisms, you can furnish a tank already so well stocked with life that the harmful organisms can't compete for space. With good lighting and circulation, you can further reduce the populations of harmful life, while supporting the beneficial life, including the crabs themselves. If one is to take as naturalistic an approach as one can to crab-rearing, and have any kind of shot at crab-breeding, which I hope we all aspire to, one must apply principles gained through many years of experience in related fields of delicate animal keeping and propagation. One of the things that all these disciplines share is to NEVER totally remove and replace with new an organism's environment and living medium, be it a flower's soil, a fish tank's water, or a crab's substrate!
Just a few thoughts........Please feel free to share your findings on the subject!