Ballistae are safer than xbow dorfs because the ballista, with its operator, can (and must, or the operator will flee) be out of range of any ranged attacks of the enemy. If the enemy only fires webs, the risks are reduced, but if the xbow attacks are too ineffective web immobilization can cause dorfs to die from starvation/dehydration.
The safe way to use a ballista against enemies is to place the ballista some 20 tiles away from the fortification at the end of a corridor, with an extension of the corridor at the other side of the fortification. You lure the FB into the corridor (on the remote side of the fortification) with e.g. a juicy door, lock it in with a drawbridge behind it. For bonus points, place the drawbridge that lets the FB in at the side of the remote corridor, with another fortification at the end of it, and a chute behind that fortification for the arrows to fall down for recovery. The ballista operator probably need some skill to be able to fire straight for that long a stretch, though, so a catapult firing into a wall with a channel in front of it for boulder recovery is useful for training.
My method for dispatching most everything that is trap immune is green glass menacing spike trap arrays on repeat (mine cart repeater). If they're too tough for my glass spikes I'll engineer a cave-in to smash though the roof of the corridor they're locked into.
While FB webs provide variety, they're strangely enough not more valuable than ordinary cave spider webs (and thus inferior in value to GCS webs). However, it's said fire AND web spewing FB webs are fire safe, and that would actually be useful (although dorfs should be kept away from fire at all times regardless...).
As far as I know, there are 2½ ways to get through a fortification:
1. Swim through a completely submerged fortification through the fluid at hand.
2. Dodge through the fortification. Apparently, this tunneling can also happen with solid walls, causing mysterious cases of militia found drowned in a moat when ordered to train inside the wall.
½. Climb/fly through the gap on top of a built fortification. Built fortification do not have a floor on top (and thus aren't walkable). This lack of a floor provides a path diagonally from above unless plugged with a wall, floor, or fortification (carved or built doesn't matter: a floor BELOW is provided regardless) above. I'm not completely sure it's possible to climb in, but flying should be no problem.
Undead make excellent silk farm bait. They'll be fired at by a GCS (or FB) regardless of whether it's tamed or not (taming doesn't apply to FBs, of course).