Is there any way to change worldbuilder to allow me to have 2 water tiles that are at a diagonal be connected, or at least let ships through to the other tile?

You mean something like this ?

LAND WATER
WATER LAND

From what i know this cant be done. It is just the way the gama handeles plots - two diagonal land plots will be allways connected as land.

You can however put a fort on one of the land plots to allow ships to pass.