Cults seem to have upsides and downsides outside of their priest bonuses, yeah.
Eternity lowers private asset productivity; Mystic lowers soldier recruitment; Shadow causes unrest with "disturbing rituals"; not sure about Apocrypha since I've only just encountered them. Haven't had any Church of Syndic in my towns yet, so not sure about them either. May well be more of them.
It does seem like certain cults (Shadow, Apocrypha, maybe others) can cause religious violence if there's significant other cult presence in a town. That can not only kill cult followers (populace) but even garrisoned soldiers. Also causes fear, which is a mixed bag - less unrest, but also less happiness.
It also looks like they may have bonuses if the favored cult or something? I started with Eternity and favor them, which leads to loyalty bonuses "from meditations" at cities with significant Eternity presence and loyalty issues. Edit edit: may just be a dominant thing? My recently-captured town with Apocrypha cult presence is now showing that they're causing additional free folk migration through proselytizing and conversion.
Then there's the priest bonuses, which are all pretty good. Eternity raises morale, Mystic keeps readiness up, Shadow prevents retreat, Apocrypha gives +100 attack on the offense and a 25% higher chance to kill on a hit (!).
Edit: And on the 200x200 craters, near the end of the manual there's a section on design compromises, which notes several issues with the large hex scale chosen (e.g. a battalion unit of ~1000 troops can't really secure a 200x200 hex).