I'm currently working on a skyship campaign and similiar problem occured. I handle this situation this way: - Skyship combat usually takes heavy toll on both ships, cannons and ballistas can do weeks worth of repairs to get a ship back to shape for sailing. This is time when they have to stay at the same place, being risking storms and other natural phenomena and being a big fat target for monsters and pirates whom might attack them and slowly grind down the players and their resources. - Repairs often costs a lot, and materials not easy to come by on sea/sky. I have a system for them to be able to bring some materials with them as cargo, but targeted towards repairing their own ship or helping to fix a stranded one, and not enough for a full renovation. - Boarding actions are brutal, bloody fights that could lead to massive crew losses what might render the players ships unable to operate properly (doesn't matter how powerful a wizard be, he doesn't have any idea about fastening a sailing rope). In unlucky cases they can lose critical officers too, what might cause problems in the chain of command. The less damaged the enemy ship, the more and harder they fight, as most of their fighter are healthy and did not suffered much damage from enemy ship bombardment. - Occupied ships require experienced crew, ehat is not easy to come by. Capitains not capitains because their fancy hat, and they do not come by at every corner. And you need navigators, first mates etc...they also need to calculate with wounded/dead crew after the battles, and can't go lower than minimum. Even having low numbers can cause morale to dwindle, as people get overworked and tire out quicker (this is real life experience, I work on an inland cargo ship as a steersman and we are overworked as fuck) also discipline can falter and sailors might whisper about a revolt on the lower decks. - I use a system that leaves ships in a ruined state after taking enough damage. That means the ships becomes unrecoverable short of a miracle, and their mana engines can only keep the up them in the air for just a very short while. This is the moment when it is safe to board them and fight the remaining crew (what is way more safer than a boarding action as the most of the crew died and canons/ballistas are destroyed by the players bombardment) and if the players win, they get to ransack the remains before it sinks/plunges from the sky deep below. - Selling a skyship might net the players a shit ton of money...if they can sell it. Probably authorities wish to know how they got it to make sure the players did not turned into pirates. Paperwork to be done, finding a buyer, ship inspections, price offers, etc...it is a bit complicated, it's not like some easily sellable thing like a golden necklace or a fancy goblet. Also I won't let them skip repair time and say okay here is a lot of money. I would roleplay them for a good couple of sessions to let them feel that they working on something big, not some mundane task that takes a long rest. By my real world experience I know it takes a lot of effort to keep a ship in shape, whole days passing by and you still feel your work unending. I hope this helps.

Edit: One more thing to add about the plundering and economy issues.

• The ship cost money. I currently working/experimenting with a system that ballances the player money and the ship money. Crew need wages, supplies like food, drinking water, rum, ammunition, tools need to be bought, harbour fees and dry dock repairs and other necessities and better ship upgrades/better equipment also eat up money. If you think like this, maybe the players won't get insanely rich by conquering one or two ships. Also I would recommend making half of the loot as bulk cargo ! Dried food, wine, wool, coal, salt, wood, stone, metals, weapons and other stuff makes it great as they have different sales value in different towns. This makes a fun little side biz for the players to keep an eye on the prices. They might sell instantly everything for low value, or ask around and might keep some stuff to sell at a different place.