NOOO My magnificant ballista tower. All these years waiting for a siege and now I find they are useless. *Cries*. *Goes to suggestion forum*.
They're not useless if you put them on the same z-level as the goblins. I have a castle with a 3-wide path, about 100 tiles long, with channels dug either side, that way, everyone needs to go down the path to get in. As the path reaches my entrance it turns 90 degrees and then enters the gate of the surface castle. behind fortifications, just on the corner so they can see right down the whole path, I have 3 ballistas. I also have 5 legendary seige operators and a big pile of ammo right next to them. Whenever anyone I don't like comes down the path, I set to fire at will and nothing ever gets close.

For extra credit, overlap the ballistas so that the ballistas behind fire over the side tiles of the ones in front, resulting in a 3 tile wide firing apeture, that way all fire travels right down the whole path, killing all in its path, and it doesn't go off the side off the path due to being fired in at an angle.
Another tip: Dig the ballista room out of hillside and build your entrance fort over the top. That way the ballista room gets counted as "Inside Dark Subterranean" instead of outside. Then when you set your dwarves to not be allowed to go outside, you can still operate the ballistas, but dwarves dont run outside to collect all the booty dropped by the slaughtered goblins.