Countering it really depends on your situation. It basically follows any approach for long range targets. First I'd recommend bringing hydrogen and moonshine (or kerosene).
The most difficult situation is where you have no cloud or terrain cover to dodge spots and shots alike, let alone close distance. You have a few options.
Not the most ideal solution, but if you can't raise or lower you ship enough, it'll work in a pinch. Try to bob up and down a bit, and keep your front pointed at them. You're going to lose components, but your engines should be safe. Rebuild your components to just before fixed. Use moonshine to help close the gap, as they're likely using kerosene to keep distance. Once you get in close, do the last fixing after their volley and dig into them. You're going to take a lot of hits, but if your engineers stay on top of things you have a decent chance.
This only works when the distance between you and them isn't all that much. If you're far away, they can usually aim high enough to hit your for a while. Since the arties can't aim up, use this time to destroy their balloon. If it's a junker (and it probably its), it should be an easy target. Then just walk them down, continuing to pop their balloon. You can use this time to try and maneuver to their blind spot and sink down to do some real damage with other weapons on your ship.
This is actually my preferred method. You usually want a ship that has pretty good balloon cover, like another junker, a goldfish or squid. With a pyra, you'll be taking hull damage, where the galleon and spire balloons don't really provide cover from the front. The mobula for obvious reasons. As you come in low, use some moonshine or kero for speed. As you close the distance they'll have to start lowering themselves to keep the shots up. Your balloon should be soaking up most of it. When you get close enough, activate that hydrogen and sail above them, raining down damage, popping their balloon, whatever. On the change that they also hydrogen and keep pace with you, still shoot them, you're now in close range and their gunners should have a tougher time hitting your components with the rapid up and down changes.
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For going specifically against a junker with triple artemis, I'd recommend the following ships:
Spire: lumberjack, artemis, field gun, other (maybe a close range gun or a flare. Possibly another artemis if you feel like making it weird). The junker is 90% balloon and 8% dreams. This makes your lumberjack (destroyer of balloons and dreams both) super effective. You just need a good shot on it. You can use the field gun and arty to reduce their disable damage, and once they start sinking things get easier.
Pyramidion: Either a gat/mortar or artemis/field gun. You could even mix it up with a hades/flak. The artemis/field gun is the perfect anti-sniper. What you're doing is applying disable on top of piercing and explosive. The front guns on the pyra are trickier to take out than most ships. You can also power them down with the hades/flak, which will also likely pop their balloon. Then you can use one of the methods above to get in close for the gat/mortar. The big advantage is the forward facing (slim profile) guns that are harder to hit.
Goldfish: Carronade and maybe some flamerthrowers or mortar on the sides. Approach flying in low to soak up shots, you have a decent balloon and your rear engine is hard to hit even if they wanted to. Once you start popping you can use your side guns to help shoot downward to give them more problems, and probably finish them with the mortar once their armor breaks, since they're mostly busy fixing the balloon.
I can't give much junker advice, it's not my area of proficiency. Galleon tends to have too much broadside, you're a crazy easy target for their disables. Squid can work great, but your engines are easy targets and your only lifeline. Once they're down, your slim armor won't last long. Mobula might be a good option, but that's not my area of proficiency either. Although the spread out guns and rear engines make it difficult to disable the whole ship.
