Boats were removed last minuted due to the desync issues, I'm fairly sure the Desync is being addressed in v2, which is being worked on alot by VRocker and the LU dev team, the boats never really added much to the game anyway since IIRC you can't swim in GTA III, I never really understood the purpose of the boats, if they catch fire you're as good as dead, but I digress, The LU team did have working boats to a point, but they found that the desync caused crashes and such, and so boats were removed for the time being, and whilst yes you can get them, Desync is a big issue with them.
Regards Orpheus