Traits have effect on ai behavior, not only on relation/opinion. Look at traits.txt there are a lot of traits with ai modifier. So your spymaster may have +50 opintion of you, that will not stop him from assassinating you.
Yep.
I already pointed out in earlier threads that my brother, who loves me at +100 relations, and who I made a duke, will still plot to take me out if he has the right traits. Relations have an indirect impact on plotting and revolts, but it's by no means the sole arbiter. You will have to learn this one way or another as you play. I had to learn it the hard way several times before the lesson sunk in; if it wasn't for the kinslayer trait, I'd probably just kill those closest to me when convenient.