Easiest way is to just use a mod to change auto pickup distance, double it from 2 to 4 and just make sure you kill them close enough to you. Since I did this, never had an issue with serpent loot again. Sure you can drag them to shore but F all that. The devs plan on dealing with it eventually, either by allowing items to float or by adding diving to the game, the latter seems more likely. There is currently a mod that adds diving to the game already.