Exactly why they weren't used often... They took forever to reload, they we so inaccurate you were just as likely to hit someone if you weren't even trying, and the range was lousy. Carrying and maintaining six fully-loaded flintlocks on a ship would be awful, if they got the tiniest bit wet they would misfire. Plus, even the small ones were heavy, they were hunks of iron that had to withstand the force of a small explosion.