Just encountered a fortress in my newest game. I took a bunch of bombers to attack it. They have a damage bonus against the fortress as they should, but it seems the fortress itself is so large that, at the closest they can get, they have a ~20% chance to hit. I believe this is a bug. I had to take the fortress down with turrets, as bombers could not hit it effectively enough to take it down.
EDIT: This is in 2.0 by the way, if that makes any difference.