true, but most games I've played there are units that hit specific units, and I bet it's for this very reason.

Ikariam for example. Slow game but well balance (well it was). Things likes catapults do not attack people. At least it didn't seem like they attacked people.

To the game, ballista don't need to attack infantry. That shouldn't be the point of it. A ballista should basically be a flying battering ram but for archer towers mainly.