Siege ships have by far the largest weapons in the game. They have to, after all. They're tasked with taking down planets, the largest targets imaginable. Siege ships must be capable of smashing through massive layers of rock and armor, in order to kill all the juicy resistance on the planet.

Why is it that they can't turn these weapons against enemies? I understand that the weapons may be too unwieldy to use against smaller vessels such as frigates, cruisers, and strike craft. What about using planet busting weaponry against the bigger targets? I suggest:

Siege Ships vs. orbital structures. These structures are immobile and defenseless. Using siege weapons, you can take them out far faster and more efficiently.

Siege Ships vs. Capital Ships. Hey, a useful (and currently nonexistant) combat role! The sheer force of siege weaponry can be used to overwhelm capital ship shields and hull. Capital ships are massive, slow, easy to hit targets, so a siege weapon should not have trouble hitting them. The high cost, high supply, otherwise extremely vulnerable Siege Ship is more than enough counterbalance to filling this role.

What about capital ships using siege weapons against each other? Well, that isn't totally unreasonable, it would make capital ships a form of counter to themselves. But, you can also say that they simply don't have enough raw energy/crew/resources to pull it off. It's more effective for them to use their main weapons constantly, rather than to shut them all down to use the siege gun.