Zornhau asked in a comment on my previous catapult post how I would make using catapults as field artillery very difficult. I'm waiting to see what his ideas on this are, though, so I'll make a couple quick notes on other catapult-related things.
One is that some siege weapons (Zornhau mentions a bolt-thrower) are designed to fire directly into and possibly through oncoming enemies. I see these as super-crossbows: use the regular missile rules, but also use the catapult minimum crew rules. Give them an area of effect similar to catapults: 1" wide per die of damage, affecting the target and potentially those behind the target, up to 1" per die of damage. They do not have a minimum range, the way other catapults do, but they also have penalties for indirect fire, the way archers do.
The other bit I wanted to mention was how to use catapults in an actual siege, destroying castle walls. I haven't worked out hard rules for this, but I think, rather than assigning structural hit points, it would be simpler to use the standard 2 or less Change Situation roll to see if a wall or structure is damaged by catapult fire; just roll the damage dice and treat both results as a situation roll. Thicker walls or harder substances increase the difficulty, choice of ammunition can decrease it (barrels of flaming oil would be extra effective against an oaken gate, for example.) Success means a section of wall 1" wide per die of damage is destroyed.