The constant AI scout ship patrols are mildly annoying, but that's about it, in general.
Except for one case - playing unlocked FFA games. When you set up your border system with full defenses, including hangers, they'll chew up the scout ships easily. Which is fine, except that any time you destroy an enemy ship, it'll reset your diplomacy with that empire to 0. That makes it virtually impossible to try and make friends with any of the AI, because they are all scouting you, and you're going to be destroying lots of their scouts. And trying to micromanage your fighter/bombers to not destroy a particular AI's scouts is difficult, tedious, and rarely effective.
It'd be nice if there were an option to either (a) Not attack a particular empire's ships, or (

Order fighters/bombers to ignore scout ships. Option (

is preferable, because not only do they target the scout ships, they'll often do so even when an invading fleet enters a system. I don't want my fighters chasing after scouts when there are bombers in-system.
Bh