I think I have negated the AI's ability with the shield boosters for the majority with ironically, raid starships. I never noticed they had so many special resistances, so they're doing fine running around destroying the command stations and the like while the AI falls into my main fleet on my friendly planet gradually, instead of having to deal with both defenses and AI mobility.
However with that said, I had cleansed a planet of heathens and only 15 shield boosters remained; a group of maybe 600 II-III bombers were already on planet and started to FRD into the group, along with a group of around 600 II-III fighters. That was quite a terrible mistake, as I thought they would be able to handle those units, and after I came back I saw that I lost almost all my fighters, and a lot of my bombers were damaged in the process, and the darned things still weren't destroyed!
So I have learned that I should never mess around with these units; even though it will cost me greater suffer to build those expensive beam frigates (rather than spamming fighters) and macro (to handle my manufactories because I generate more metal than crystal), I think I should be able to minimize the frustration.
As a side comment, why don't raid starships have mine immunity?