I haven't seen a squid since about a week after the patch that added them. I have a "water wall" around my base, and I frequently scan the large "ocean" outside my base for movement, but no luck.
Squid cannot swim upwards, so they tend to sink. In my personal experience, they don't seem to spawn well in shallow water at all, so you will likely have to look down deep to find them.
The wiki mentions that an easy way to find squid is to stare into a large body of water and rapidly hit the fog distance key (F3+F).