Siege weapons were rarely used in pitched battles. Sulla set a precedent when he used ballistas to punch holes in the Pontic phalanx during the First Mithridatic War. After that, some daring commanders would use ballistas with their troops, but onagers is mostly unheard of. The main problem is probably accuracy. Carroballistas were more accurate than the 18th century musket, and could punch through 2 men fully armoured. Onagers, on the other hand, were hard to aim properly and considered to be a lesser quality weapon. As a result, they weren't really used that much until the 3rd century, when the number of skilled engineers in the Empire began to decline.
I suspect that another reason siege weapons were rare in pitched battles was due to their immobility. Despite how it is in RTW, most siege weapons took great time to position and were difficult to move-but the carroballista, being on a cart, was the exception. Also, the terrain would have to be perfect for using siege weapons. One cannot put ballistas in the front line, as the expensive equipment can be easily damaged. You would have to put them to the rear on a hill that would have to be in the perfect position to hit the enemy and not your own troops. And once the melee begins, all firing would have to cease so you don't massacre your own men like a Persian satrap. So, daring commanders aside, siege weapons first and foremost use- and most practical- was besieging. When it came to the battlefield, only light artillery-carroballistae- were used.
His ego nec metas rerum nec tempora pono:
Imperium sine fine dedi.
(P. Vergilius Maro, Aeneid I. 278-79)
We are all, so far as we inherit the civilisation of Europe, still citizens of the Roman Empire, and time has not proved Virgil wrong when he wrote nec tempora pono: imperium sine fine dedi.
(T.S. Eliot)