Although the junker has one of the easiest balloons to hit, it's also one of the easiest balloons to get to. One of the bonuses of the standard junker player positions (helm, top deck by the side guns, front gun and hull, and below deck) is that there's a good amount of redundancy. In most ships, everyone tends to cover something different. But on the junker, you can double up on some of the core components, in particular the balloon and hull. The pilot and top engi can get the balloon, while the pilot doesn't even have to move from the helm; while the front engi and top engi can also get the hull. In an emergency, you can also get the gunner out from the bottom deck to help with the hull.
The other issue with using carronades against the junker balloon is that those guns have a small downward arc. If you're not right on the balloon, the junker will still be able to hit you with it's guns (typically the hades, or the gat/mortar). If you're right on the balloon, you have some safety, unless you're in something like a pyramidion. The top guns are near the top of the ship, which means you have to leave a meaty part of your ship in their gun arcs if you want to keep that balloon in your sights.
