That people with good relations don't DoW? Yes, but it's a qualified yes. Friendly nations don't DoW, and hostile ones do, but over the course of especially the GC, all coreligionist relations end up at +125. The AI sees this as being friendly. No real problem, you might say, but states with different religions have relations which normalise to +100. The AI also sees this as being friendly. So it stops DoWing. The other contributing factor is the AI's tendency to have randomly large alliances. The AI won't DoW unless it is of equal or greater power, in its alliance, than the alliance it is DoWing. The end result is, after a long enough period of uninterrupted play, say 150-200 years, AI DoWs slow to a trickle.
When you reload, however, that AI doesn't look at the relations it has when DoWing for a short period, and so it only considers the normal criteria - borders, relative power, and CBs/cores.