The silly Pirates nerd in me is trying to think of a reason to not place all of them. I assume since each token is considered a UT that they’re not considered “available gold” for endgame conditions? If you know you have a lead but a weakened fleet and your opponent has an HI Raider, you might want to end the game as fast as possible, in which case less turtles could help.
A physical limitation is the only thing I can think of, either a lack of turtles to place or (somehow?) not enough space to place them.
Even though they head toward a specific player’s home island, they don’t actually belong to that player until they arrive, so they won’t count toward victory and won’t do anything to prevent the game from ending.