The problem really becomes when there is no foreseeable counter to them. (excluding more carronades)
Merc/Artemis and mind your distance. Everything else is upon your crew actually hitting the gun, the map and captain teamwork.
I don't have the same issues especially since the new patch where we have more viable setups than gat/mortar.
Fighting against very experienced captains is always hard. The other captain can be a new guy with the right ship, it doesn't matter as long as he/she does communicate. This is how I started and anihilated better teams, I had a very good captain on my side telling me what to do. The carronade only amplifies this, since the hardest part of it is to positioning your ship correctly imo.
Also, fighting good squids is hard, there are so few of them that it is really difficult to develop tactics.
I spent all night trying different set-ups (a lumberjack/merc/artemis spire seemed the best, followed by a regular mobula build) and in the end it never mattered. Team with the most carronades wins...
I think fighting a carronade ship is less about the ship/layout and more about position, vision and usage of cover. Just don't take the Junker.
I consider a Merc long range Spire a hard counter to carronade ships. If it didn't work, then the enemy was able to outsmart you. Which isn't something to be ashamed of when you fight a lvl 10, somebody who practiced outsmarting people.
I vehemently disagree on "most carronades wins...". No, I was able to fight two blenderfishs WITH A JUNKER, while my wingman was busy chasing his tail. The only thing I had was a trifecta with two artemis' and an able crew. They couldn't even kill me once, their gun was disabled before they came close. They were obviously not lvl 10 captains. But still, I had a Junker...