Welcome back
There's no option for turning them off (except for playing on diff 5 or lower, but that's not really an option per se), but they've seen a lot of changes lately to make them at least more interesting (specifically, there's more variety of them, so they don't all cheese you the same way). And in general you can either:
1) Kill all the guard posts before bringing in the full fleet.
or
2) Be able to do what you need to do without triggering the eye.
The ones on the AI homeworlds are a different story as of 6.002, they're just brutal. But lots of stuff on the HW is brutal, you may actually prefer the eyes to the other stuff that can take their place (and sometimes do; the HWs don't always get them).
One other thing is that AI types vary in how many eyes they get. Turtles, Teleporter Turtles, and Technologist Turtles all get a lot more than everyone else. Shield Ninnies, Grav Drillers, and Peacemakers get slightly less than the turtles (twice the normal).
On the other end, Mad Bombers, Neinzul Youngsters, Vicious Raiders, Extreme Raiders, Technologist Raiders, Scorched Earth, Attritioners, The Tanks, and The Cores all get half the normal amount.
From there, it's scaled by difficulty, so diff 10 gets 1.66~ as many as diff 6.
