After a lot of swimming around looking for squid, I have given up and tested around which mod was affecting it...
It turns out, that Fairy-Lights seems to disable the natural spawning of vanilla squid completely.

Haven't noticed any other entities missing

-Fuzzi

Pardon my late reply, but have you tested without fairy lights?

I definitely checked that last time and it was working without fairy lights,
but just now, fairy lights wasn't the problem and something else seems to cause the issue.
I could have sworn I tested everything last time, but we've also upgraded some mods since then, so idk...
I'm confused now