I experimented with metal ballista arrows. My conclusion: Absolutely useless.
Basic no-quality iron armor can almost completely deflect all shots from a ballista. Exceptional quality ballista, exceptional quality ballista bolts made from: silver, copper, bronze, iron, steel. Best I got was mild bruising, nothing even remotely fatal. They healed before I could even get another shot to break through enough to do more damage.
Even on unarmored targets the ballista is ridiculously weak. It shatters some bones, but doesn't hit everything in its path and rarely kills anything. I had a siege operator fire off 57 shots (thats how many shots my 20 arrows lasted, 4 of each metal type - all high quality) through a 3 tile wide corridoor with a wall and ditch at the end (to recycle ammo) and 20 unarmored recruits standing in the hall. 11 of them were injured severely (shattered bones), 2 of them were dead (bled to death), and 7 of them were completely unhurt. Several of them had been hit numerous times without actually dieing, and many of the shots only hit 1 part of the body - shattering one bone, but leaving the dwarf otherwise fine.
I then reloaded the game and released one goblin bowman I had captured in a cage trap against the 20 recruits. 4 of them died before they wrestled it to death. So: One goblin bowman = twice as dangerous as 57 shots from a ballista. Woo?
Siege weapons definitely suck this version.