ORIGINAL: Yaab
In the game, all 2Es are idle, because there is no interdiction missions for them, so you pound LCUs with them. It sucks, it is unrealistic, it is game-breaking etc. Wish 2Es could at least target those immune oil/resources or inflict friendly casualties when on CAS missions. More house-rules than clicks. Meh.
You need to be more imaginative. 2Es can do far more than bomb LCUs or not bomb LCUs. And nothing is "game breaking." Please.
2Es can attack Cities in all of those missions except mining. They can attack Ports. They can attack AFs and destroy supply. They can train pilots. They can be kamikazes.
You can HR anything you want, but slavish devotion to real life will break the balance of the game. Supplies and fuel move FAR too easily through jungle in the game. Aircraft repair is FAR too easy in the game ("Spare parts? Make them from rice balls.") Bases are taken in a destroyed state and are fully operational in a couple of days. Wounded men heal in a week. And on and on. Some aspects of the abstraction speed op tempo up, some aspects slow it down. It's a dance.
For the Allies at least, plane counts are fixed at historical numbers and that has to be factored into use. But 2Es can't be used in the CAS role to any great extent for reasons I've spoken to many times, and you mention. There are no bridges to bomb. There are no rail marshaling yards. There are weak anti-personnel weapons in the game. Bombing LCUs at whatever altitude your risk profile likes is an alternative. HR that away, and then yeah, 2Es get left on the ground more. And the balance shifts away from the design. You can do it, but be careful forcing the issue. You may not like the spin-offs.