You have to address the root of the problem, which is the fact that snubs and caps are able to do damage to each other at all. Capital ships are grossly overpowered against snubs because they were balanced against other caps. Bombers, while they were not exactly overpowered in that regard, still have extremely powerful weapons that could instakill anything smaller than a gunboat, because they were designed to counter capital ships.
The only real solution to this is to redesign capital capital ships entirely, by giving them slower weapons and slower movement. Then they would be impractical to use against snubs. On the other side of the fence, bombers and their assorted weapons of mass destruction would have to be removed entirely as a concept and repurposed in a meaningful way.
As for dual razor SHFs being able to instakill fighters and other similar shenanigans, turning nanobots into hull points just like it was done for battle cruisers could be a viable solution.
