Squids naturally spawn in the range 46 <= Y < seaLevel. The server options provide no way of changing this.

This sucks for customized worlds, because if you have a seaLevel lower than 46, you will never get naturally spawning Squids.
Please consider adding this to mainline Spigot.

 

Alternatively, could this be solved with a plugin? Being able to replace a method in net/minecraft/server/EntitySquid would do the job, but as far as I understand the Plugin API, this isn't easily achieved.