Originally posted by Governor:

You should get 100% back on almost everything. Just got to be careful that things do not roll or sink out of reach

Originally posted by Arcangelo:

Items like nails usually sink, check underwater. Always destroy your boat in shallow waters.
Valheim isn't a buggy mess at all for an early access title.

Agreed. The most common loss from a boat for me were the nails. Sometimes in water deeper than is reachable.
If in shallow water, close to shore, you can build steps/ladders up to a height where you can jump off and dive deep enough to grab them.