I believe the net fishing logic changed a few years back. It used to be that waiting too long would result in all fish being dead, but I believe it was changed so fish died over time, possibly base on when they entered the net.
When I've used net fishing (which I haven't in the new version) I tried to alternate between checking nets in the morning and in the evening to get approximately 1½ days in between the checks.
While I've had a rather limited experience with active fishing in the new version, I've had problems with it being an all or nothing affair, i.e. either you get nothing (most of the time) or you get a single large fish. This makes it difficult to sacrifice fish, as you don't really want to sacrifice the single salmon you caught after 3 days. While I did fish I tried to sacrifice the last bit of a roasted fish (so the amount was about the same as a cut of meat or less), but I've seen it said that sacrifices of prepared food went to the spirits of the forest, not the waters...