how does one change 90% of the water without exposing animals on the upper part of the tank to air for too long?
Accumulation of toxic compounds is a possibility in our systems, although it is moderated by heavy skimmer, activated carbon, and 30-50% water changes.
90% water changes would be very difficult, mainly due, not to the fact that corals are out of the water, but rather by the fact that you will have a hard time matching temp, salinity, and other conditions. Without very close matching, you risk putting your animals through some fairly heavy stress load. Not something I recommend. 50% will still frequently expose a few corals, but as long as your halides aren't beating down on them while exposed, that tends to matter little to most (don't expose sponges!).
Wade