counter-siege tactics mate. build your offensive engines and right when they're built put them into reserves, repeat until you have 4 of them, place all before entering the "lead assault" and, boom. You got yourself return-fire for the defending ballistae...
if you are patient enough, just push for the most OP bombardment siege engines, stack 4 before deploying all at once and they'll make a short life of any defensive engines quite fast. I generally clear enemy defensive engines before assaults, or place at least 2 or 3 counter-fire ones before ever engaging. If patient enough I'll spam 4 trebuchet and take down both walls before assaulting.
If you know the scene in which the siege happens you can also apply tactical builds that are much more efficient than brainless spams of all 2 towers + rams. Sturgian castles are mostly built with significant kill-zones for rams, so I never use them in sturgia, instead I either take down walls or use 2 siege towers. If they have a strong engineer governor that keeps replacing bombardment too fast, I use only a single siege tower and let stairs for the zone closest to their bombarding engines. The logical thinking here is that you can manully lead an early assault on the ladders and basically rush for the defensive engine towers. It saves a lot of casualties.
Summing up, you must understand the layout of the place you're attacking, build proper engines against said settlement and use some tactical decision making as to how you employ them, when, etc. It's also important to note that you should always be aware of switching your party screen priorities for best troops for sieges. The priority for deployment goes from top to bottom, so the top lines will always spawn, while the lower ones will be on "reserves" for re-spawns.
again, some scenes the siege tower against t3 walls sucks, while the ram remains the best choice. Other scenes rams suck and siege towers suck for t1 walls, just spam ladders. t1 walls are really short and quick to climb from ladders, except for one of the imperial layouts which puts the ladders almost horizontally, making you take ages to climb on one of the sides. As for siege towers, you gotta make sure they are fully covered from all angles once they are placed against the walls, otherwise it's only worth it if the tower itself doesn't have ladders in it, otherwise your men will be sitting ducks while climbing. So on so forth...
To me the real issue is the bad UI for sieges and how we must resort to gamey "techniques" to make those really "tactical" and proper. Why would someone build their engines under range from enemy fire? That simply doesn't make sense.