Thanks for the detailed feedback! That's really weird on the button thing, I'll have to take a look at that. It might have something to do with Godot auto-sizing. I had intended to add more options including resolution/windowed mode so perhaps adding that will fix the issue.
I like the idea with the healing system, I've been thinking of how to do it better. I didn't have time to make health pickups/vendors so that is part of the reason I did the slow regen system instead, and I thought it would reflect crew making repairs to the ship as you sailed. But I think either something like you suggested with repairs at ports or by making it an ability that locks you in place/prevents you from moving while you repair might be a good way to not make it frustrating but also make it more balanced.
The ocean definitely needs some work to be not so sickening, I was worried it would be that way and it seems I was right to worry. I think that's a great idea about adding vertical waves here and there or I may just replace it completely. I've seen some people make 2D water that in way has reflections/particle effects so I may try something like that or if I want to keep it more pixel-y, I think your idea is probably the right way to go.