Not sure it will be an issue until one gains the highest technology levels : checking the work-rate/capacity equations, the fleet should never fill fast enough to get back to port within the hour (the exception being sloop/cutter fleets due to their small 30 crate ship capacity).
That said, I do like the idea of a 'carelessness' penalty for those who don't do their sums first and add a 'slower-filling' ship type to their fleet, or reduce crew numbers, to keep it over the hour. We do the same for trade fleets, so its not rocket science.
But, for fairity's sake, if the fishing fleet cant use the merchant's bonus of auto-stop when endangered.. perhaps fishing fleets should not require one to work?