#1 - April 30, 2013, 9:02 p.m.
When you enter the water, they disappear, and you have to conjure them again when you get out of the water.
They used to swim with us. 
I don’t see anything in the patch notes about it.
Mini pets and water :(
#3 - May 1, 2013, 12:17 p.m.
This is intended behavior, this is to prevent mini pets without underwater animations from being used or summoned in water.