Seriously? Bumping after 15 minutes?
You should build both, because setting a catapult on repeat builds up Siege Operator without using up labor-intensive balista bolts. Note that neither catapults or balistas have a parabolic shot. This means that if what you want squished isn't on the same zlevel, it's not going to get hit.
Balistas can shoot through fortifications, but the same rules apply -- the further it is from the fortification, the more likely it is to get stopped by the fortification.
As for what's better and why ... uh, none of the above? Siege operation is rather hit-or-miss, for a variety of reasons. For one, it's not aimed. You can set up a balista at the end of a very long hallway have have a decent chance to wipe out gobbos (and dwarves...) that are in the hall, but out in the open? Not so much, and if you're already funneling them through a long hall, why not just trap the hell out of it and be done with it?
Another problem: Siege Operators are civilians. Yes, that's right, those same little girls who run in abject terror when a gopher shows up. Again, unless you can hit them from very, very far away (such as the aforementioned why didn't you trap this?! hallway), they're going to run away the moment they have a decent chance to actually hit the gobbo.
Oh, look, another problem: You know how crossbow bolts have this annoying tendency to bounce off of clothing? Well, those same algorithms determine if a balista bolt pierces clothing/armo (unless this has been changed?)
This isn't to say that you can't engage in the wholesale slaughter of gobbos using siege equipment, you just have to be aware of these issues and take steps to adjust for it, but you probably don't want to use balista's unless you want to. Traps are much better, as is a well equipped and trained squad.