I think there should be a respawn timer for when your ship sinks and it gets longer each time it sinks and gets shorter the longer you sail without being sunk. I don't think the timer should ever be more than 15 minutes. Perhaps no time for first time, then 2, then 5, then 10, then 15.

I also think ships could be repaired and resupplied to minimums at outposts given a bit of gold and time. This is better than scuttling the ship for the same reason to accomplish the same thing.