in my limited experience, flaming projectiles from onagers are not worth it; they are waaaay too inaccurate, and most of them missed the town itself...
it would of course be a whole different story if we knew exactly how much of an impact on morale they have.
However, since it's likely that that morale penalty only applies while they're under fire, it may not be worth bothering, because their lack of accuracy makes that kind of impossible.