I agree with the OP, running a ship full of guardian modules/weapons is zero fun when a Hunter shows up. Can't avoid it, can't fight it, can't escape it. Feels like bad implementation of game content from this seat.
However, I do wonder if FDev are creating a problem so that they can then solve it with some sort of blocking utility module later on down the line.
They are certainly over powered at the moment, and seem to be designed for interdiction, which is an awful mechanic to begin with and just annoying when it can't be countered. They are brutal enough in CZs, but in interdictions they are fun-police dialed up to 11.