I might have been lucky, but so far serpents have been quite easy to not fight for me.
If you have some wind in your sails, you can just outrun them, and they get maybe 1 hit on your boat.
If you are paddeling and you get away from their spawn location far enough, they will stop following.

I also had one run away the moment i shot an arrow into it.

Boats are quite durable so as long as you repair it before and after you sail, you should be fine.

The real problem is when islands are too close together, and you have to move between 2 nasty biomes.