In my experience everything took a hit. Two things seemed to survive better than anything else though, Fatheads and Scuds. Looking back now, before aeration, I think even the fatheads and scuds were dying as well just not as severe. After aeration I seem to have far more scuds and fatheads plus I see a lot more "bugs" than ever before.
Someone else may have a more eloquent answer, but here's my take on the bacteria. There are two types of bacteria, aerobic and anaerobic. Aerobic digests muck MUCH faster than Anaerobic. The more time your pond spends with low DO or, if your bottom water is anoxic, the more time you depend on anaerobic bacteria and it will never keep up with muck build up.
Keep This Forum Viable, Read Pond Boss Magazine -
America's Journal of Pond Management