I have an idea or two.
These guns could be beaming microwaves.
That meaning the beams would heat up the part of the ship they would be targeting causing it to melt, for an example if the would target a small ship they would melt it in about 20-30 seconds if the small ship wouldn't be able to get away, but in combat with a bigger ship it would only target parts of it therefore weakening it for an example destroying its canons or hyperdrive engines so it wouldnt be able to get away. You could even implement a computer scanner that would reveal vital ctructures on enemy ships like oxygen containers, communication arrays, radars, targeting system sensors. The guns would be weak, but if a group of these guns would target the same thing it would be devostating. It could be also used to heat up incoming missiles so they would blow up before raching your ship or any other for that matter.