My current playthrough on 1.5.9 is about 14 years in. There has been a total of 5 rebellions. Myzea, Onira, Danustca, Husn Fulq and Poros.
I own Myzea, Onira, Danustca, Husn Fulq. I couldn't get to Poros in time.
Onira and Husn Fulq changed hands probably dozens of times before they rebelled. Literally every time I looked they had changed hands. Their prosperity was down at about 1000 when I picked them up.
Onira especially at one point went to almost 0 loyalty and bounced back up to 40 but still wouldn't rebel. Finally when it did, I was in Vlandia and literally dropped 400 horses in one go to make it back before Monchug showed up.
I think the faction policies have a lot to do with chance to rebel. Khuzaits have grazing rights early on which gives them a loyalty buff. But in my current game they've debased their currency - after which half their conquests rebelled.