Nixe? Like water nymphs? Is this a mod you're using, or have you simply misspelled "neck"? Necks don't do a lot of damage, so I'm wondering if it isn't the former. Creatures don't do damage to things unless you've gotten close enough for them to spawn in and become "active", and you'd have to be ignoring a neck for it to have enough time to ruin a boat. If it is just necks, you might consider leaving some wolves nearby. They'll handle necks no problem.

if it bobs up and down hits any rock it will take damage

Make sure to park your ship at a depth to deep for walking mobs and rock slamming in the waves, and away from swimming mobs.

Ships were destroyed by Nixe


Do you mean neck?

Put down a workbench repair your boat and kill the enemies around the area.
If this does not work place your boat close to the shore and destroy your boat with the axe and take the resources from the boat with you and build again whenever you need it.

I had a new long boat destroyed by neck. Definitely needs fixing. In the mean time, destroying it and carrying in your pocket (!!!?) is the way to go.