Historically ballista's were a piece of siege equipment that needed proper training and support in order to function. The mere act of winding one up to fire could easily exhaust an untrained man and it can take a lot of time to fire even a single round. That said it was superior, especially in anti-army capabilities, to the catapult which often had an even longer reload time, was less accurate, and packed less power except against buildings. So you would typically deploy ballista and scorpions behind your front lines and have them target enemy fortified formations to break them with ease.
However with the rise of the medieval age it became very hard to create and upkeep a ballista especially with improvements all-around to bows, armor, shields, and other forms of siege. Onagers were easier to create and took much less training and, eventually, trebuchets and mangonels simply outclassed the ballista in everything that it could possibly do. That isn't to say you never saw them; but they basically only got deployed in places like road checkpoints where they could be fairly assured to only be used for anti-person purposes. The crossbow was basically the true final nail in the coffin though as it was basically a mini-ballista that anyone could use, didn't exhaust anywhere near as much, could get through armor and even shields potentially, and was far more portable and capable in general.
Come the Renaissance there was simply no reason to consider ever using a ballista since any niche they could possibly fulfill had been replaced by better/cheaper/simpler siege, crossbows, or basically anything else. They were a novelty at best and the rise of the musket and cannon ensured it could never possibly rise up again.
For the same reason that Captain America is ridiculous since the shield fell out of favor as soon as firearms became a thing... ---
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