There's a thread on these forums that deals with the siege towers missile capabilities. Apparently, it works so long as the unit inside/pushing the tower is NOT a missile unit. Just set the tower to fire at will, and it'll open up.

I think the different types of tower are made depending on the size of the wall. For large stone walls you get those ones that look armoured, though they catch fire just as well as the other ones! Apparently the big ones fire ballista bolts, and can be devestating. I'm guessing they also take more build points.

I've never tried it, but apparently you can just wheel the towers up near the wall, halt and let them open fire - they can pretty much take out a whole unit that way. Now why doesn't the AI ever do that?