Might be a system-specific issue - you can find multiple 2+ hour long VODs of NTT.
Nuclear Throne is a 32-bit application so it cannot use more than 2GB RAM at once (which is the point where it should be crashing).
Hard to recommend any particular solutions, to be honest. I know that the base game had a tendency to crash at 0-1 boss intro, but I seem to have fixed that without figuring out the source of problem. Could be that something is only amplified enough in coop mode, but it's hard to tell if most people don't have the issue. If it crashes at some particular points (e.g. boss intros), that could provide some clues.