Absolutely. Not often, but it did happen. The not often reason is simple. A fort is a tough nut to crack, and requires a force so large you need a fleet to transport it, and most pirates only had one or two very small fast vessels. We have this movie fed picture of pirates fighting men of war in frigate to frigate actions with both sides having a 30-40 gun purpose built warship, but a more typical pirate expedition involved stripping down a small merchant ship, putting a few cannon on it and because the ship is so light being able to catch a heavily laden merchant ship or run away from a naval vessel carrying numerous guns, enough men to man them, and enough stores to feed all those men.
The best example I know of a Pirate who rose above the typical and raised enough men to take a fort was Henry Morgan. Morgan (the man the rum is named after) was a Welshman from a family of soldiers and mercenaries who either got a commission in a Caribbean expedition Cromwell sent to attack Hispaniola or went there because his Uncle was Lieutenant Governor of Jamaica.
Morgan served in several privateering expeditions (legal pirating licensed by the English government) and worked his way up the ranks till he was famous enough to command respect from all the pirates and pirate captains in the Caribbean. In 1688 he led an expedition to sack Porto Bello, the third most important Spanish city in the New World at the time. It was protected by three forts, Morgan sacked two by attacking with surprise and getting in the forts before the Spanish defenders could mount a defense. The garrison of the third fort surrendered when they realized the first two forts were taken.
In Morgans attack on Maracaibo the next year (inland, protected by a fort guarding a narrow outlet of Lake Maracaibo to the sea) the Spanish abandoned the fort and attempted to trap Morgan by lighting a long fuse and setting off all the gunpowder in the magazine. Morgan smelled the fuse burning and snatched it out of the magazine, saving himself and his men and creating another staple for movies. He then sacked the town, ransomed it's wealthy inhabitants and fought off a vastly superior fleet of three Spanish warships that bottled him up in the inlet by turning his own flagship into a fireship. This was one of the most audacious attacks I have ever heard of.
In 1670 he sacked a Spanish fort with a fairly large garrison and sacked Panama City, a critical Spanish possession and major link in their treasure transport system. Morgans men were undisciplined in sacking the town after defeating the Spanish troops defending it, and they let a Spanish galleon sail out of the harbor full of valuables. That was Morgan's last great adventure, he retired from pirating/privateering afterwards and became a gentleman, living on a large plantation in Jamaica and drinking himself to death.
A good pop history type book on Morgan is Empire of Blue Water by Steven Talty. I figure if you are asking from a video game you might like this better than a dry straight history text, but I would caution you this book was written by a journalist as historical entertainment so it should not be considered the final word on Morgan, particularly as Talty claims Morgan was definitely a member of Cromwell's Hispaniola expedition and I don't know if this has been settled.