I'm not sure why, but Ion Cannons are no longer firing on new nests that are revealed/created, despite being enabled in all settings and having sufficient cannons ready to fire.

Sorry, I'm not sure what should I do now?

I was hoping there was something obvious I was doing wrong honestly.

Yes, yes there was.
How do I keep forgetting there is an auto-targetting research?

"...are no longer firing..." indicated that you have already researched automatic target acquisition und that it suddenly no longer works.
you dit not say "its does not work after starting e new game." ;-) But OK, I wouldn't necessarily have thought of that either.

For my scenario, the cannons do autofire. I won't say they autofire the way I want them to but they ARE working.