Pirates are definitely a threat.

Not the Somali and Malay pros, who arm themselves with AKs and RPGs, you're not likely to be able to fight them off successfully no matter what heat you're packing. Its the local home invasion/hijacker/druggie types who come aboard when you're anchored in some secluded cove to steal your stuff, or your boat, you have to worry about. You're in a remote, wild place, you can't hide, you're unfamiliar with the area and no one knows where you are, or exactly when you're due back. That makes you very vulnerable. In Florida, boat thefts (for use in the drug trade) were becoming a serious problem until the authorities started cracking down. The owners were usually never found again, and the boat usually turned up later, gutted and abandoned. after one very profitable haul.

For the blue water cruiser, I do not recommend guns. Foreign governments are not hospitable to them, and Customs people know where you're likely to be hiding them. There are yachtsmen in jail in Jamaica because one cartridge was found on their boat.In the few countries that won't arrest you on the spot for having one, the paperwork , and the fact they are confiscated until you're ready to leave, make them more trouble than they're worth.

I have a friend who used to spend some weeks at a time fishing in the Ten Thousand Islands area of SW FL, where the Glades meet the Gulf of Mexico. (Check it out in Google Earth, its a remote wilderness of narrow channels, salt water marshes, and mangrove swamps, only accessible by boat.) He was on a shallow draft houseboat suitable for navigating those waters, but he never went alone and he never went unarmed. The area is far from towns or roads, and is a harsh environment for anyone without a boat to sleep on. Besides the drug smugglers, the place was frequented by fugitives who blended in with the sportsmen who came to the place.

I used to sail to small offshore islands or remote beaches and camp out, I might be only a few miles from civilization, but I might as well have been in the Outback. A boatload of teenagers cruising the beach is probably benign, but if they're not you have nowhere to run. I was always armed. This was before cell phones, but they would not have helped much.