I have researched Auto-Targeting along with the Orbital Ion Cannon. When new hives are discovered via a radar they are not marked for destruction and the Orbital Ion cannon has never fired automatically. Does anyone have any ideas as to if this functionality isn't working anymore?

How many ion cannons do you have in orbit? In version 1.5.2, a new mod setting, "Minimum Cannons Ready Before Auto-Targeting" was added, which allows you to keep a couple ion cannons always ready for manual targeting. This could be what is preventing automated targeting.

I've got 252 cannons in orbit. It does autotarget, but never more than one cannon at a time. So the map looks like this. https://www.dropbox.com/s/0ri8stk2907fb7d/Screenshot%202018-03-22%2018.23.25.png?dl=0

All that clear space to the west was cleared manually. The east is how it looks if I don't clear apart from around the rails. Railworld, so they don't build new nests much.