The location says investigators can ONLY get there through devil's reef, but the sailor says he can move to ANY aquatic location so we were having trouble deciding which takes precedence. We figured that if Y'ha N'thlei was an exception to the sailor's movement then it would have said so on his card. But we wanted to get an official ruling.

It says so not on his card but on the IH board at Y'ha-Nthlei itself:

"This is true regardless of other game effects"

dj is right. It is usually unwise to put a specific exception on a character's sheet when there could be more exceptions down the line with more expansions. Better to put it on the location in question.