If you look on real historical use of ballistas, they were used to shoot one single, heavy targets (ships, siege towers, battering rams, wooden pallisades where archers hide etc.) rather then just firing somewhere in the middle of some people running around.
Reason is that a bolt (no matter how big it is) does not really have any "area damage". It hits a single target very hard, maybe crushes through and hits someone hiding behind an obstacle, but that´s it.
Therefore I´d prefer that ballistas:
- should get very high damage against single target (but only little damage against buildings, maybe except gates)
- a very narrow, but strong area damage (like 1 - max. 2 meters in real scale)
Their use would then be:
- shoot on enemy siege weapons
- shoot on trolls, mumakils...
- shoot on units in defensive block stance, for example tower guards (due to the small but strong area damage they´d be hit much harder then troops in lose formation!)