I know this is against common wisdom but I'll put it out there...
An iced over pond will be warmer than one kept open with water movement. An iced over pond is about the only time a pond will stratify. The temp just under the ice will be say 32F while at the bottom, hopefully, 39F. Water movement would cause the entire pond to be uniform in temp, probably close to 32F.
Only pure water freezes at 32F. Most ponds have some natural salt from whatever water source is used. So with water movement you could get the water temp below 32F and still be ice free.
Gas exchange, yes, in a perfect world there would be great gas exchange. Trading low temp for gas exchange imo might not be a good deal. And the smaller the hole the less the gas exchange, so how much benefit is actually being seen would be debatable. But like Michiponder said, it depends on the pond. We're talking about the absolute limit of life here. Things can go either way and it's hard to predict which is going to be the best choice for a given winter.
My ice experience comes from upstate NY. Only a memory now.