Historically, cannons attained widespread use before handguns. So if you envisage having pistols and muskets freely available to players, it makes sense that there would be ship-mounted artillery as well.
Our RPGs are chock full of anachronisms, so I wouldn't worry about your 50-year timespan of access to these strange new islands.
I use the Golarion setting as well, but added a few personal touches. I added
the city of Freeport (from Green Ronin) to the setting, putting it some 100 miles offshore from Magnimar, near the edge of the islands refered to as Old Azlant.
One thing you should keep in mind about cannons is that they are very heavy. Large cannons couldn't be mounted on ships until they began using cannon ports along the lower decks. Putting heavy cannons on upper decks would make ships unstable, and liable to flip over with the slightest wind. As a consequence, only lighter cannons were used on upper decks, and these weapons had at best an anti-personnel role. The heavier cannons that could damage or even sink other vessels were invariably installed on lower decks.
IMHO, boarding actions are more fun to run with a group of players than maneuver and gunnery actions. When a ship is maneuvering, you only have one player or NPC, the ship's captain, acting at a time. Sure, you could also have various players or crew NPCs rolling for individual actions, like setting the sails or reparing battle damage or sniping at opposing crewmembers (at long distance), but with boarding actions you can let them run wild with the full gamut of combat options.
Of course, the presence of magic almost makes ship's guns redundant. Imagine what damage a few well-placed fireballs could do to a ship's rigging. Or what havock summoned sea monsters could wreak on other ships. If you don't want the players to find their ship suddenly smashed to pieces, and their characters scrambing for water breathing spells and potions, you'll need to moderate the ship-to-ship actions, relegating maneuvering and artillery duels to narrative sequences, punctuated by boarding actions or narrow escapes.