That is precisely what I will do. A lot of MOC ships only have broadside cannons. If you have six boats each mounting a ballista like the one on the skeleton ship attack on the front, the enemy ship would need six turns to destroy all of them. You would be able to have 21(6+5+4+3+2+1) firing passes. You would be able to heavily damage, if not destroy the ememy ship.
I think rowing should be made a factor of overall speed. Boats would be even faster and deadlier with this advantage. Basically, boats would be used in hit-and-run tactics. If you don't get hit, you won't get sunk. Of course, one 24 pounder on a ship would have more than enough firepower to sink a boat in one hit. Also, I think it's possible to mount a 24-pounder onto a boat. TLG has done it on 6241 (Loot Island) and other sets.