The short gill plates can be due to many many factors including oxygen. That defect shows up in hatchery fish as well so i wouldn't say low oxygen is definitely the cause. This is about salmon but it kind of explains it.
http://www.ekoi.lt/uploads/docs/AZL_...-316%20psl.pdf
I've only seen that on rainbows a few times, it occurs a lot more in brook trout on some streams (I'm pretty sure its inbreeding related in those cases, as the genetic pool is pretty shallow for any fish when they got there in a fisherman's bucket 50 years ago).
As for spawning, fish will try even if conditions are marginal. The eggs (rainbow trout in particular) generally won't hatch in standing water as the eggs require good circulation and gravel free of mud and silt. I watched some rainbows trying to spawn on a muddy mix of shale and twigs in a beaver dam last spring, pretty strong instinct to give it a try.
And for winter killed fish, often as they rot (and bloat) some will show up on the surface or washed up on shore. You may see white bellies on the bottom while boating otherwise. Too bad the ponds winter killed, it was a long winter. I'm pretty sure one of my favorite pike lakes winter killed at least partially this year as well. Will take a few years to recover.