Bah, comparing FS2 ships to present day products of aerospace industry is very moot. The surface of airplanes is smooth because it produces predictable laminar flow of air. No need for that on space. The surface textures can be whatever is easiest to make, so if Herc 2 uses some specific armour material that naturally has a grainy surface like that, there's really no need to use too much effort to smooth it away is there?
And no, the F-35 doesn't have rubber-like finish, just matte paint on the surface, which is either aluminium or composite material.
To me, FS2 is one of the games where I don't really ultimately care what is realistic and what is not. Sure, if realistic looks good and works as good or better than unrealistic ones, then I prefer that. But in cases like this, looks are all that matter to me. Mainly because we can't really know what would constitute as "realistic" in an ultimately very unrealistic game, which means that calling something unrealistic on real-world basis like the presented argument of airplanes being smooth makes no sense at all.
Of course, FSU team is open to new stuff. If you think you can make a better Herc 2 texture, do it and show it to us. If enough people like it, it might be included in the following MediaVP's. If not, alternate textures are still useful because it really is unrealistic to assume all ships of same type would have exactly same finish and painting. It's very unlikely all Herc 2's come from the exact same assembly line. There are bound to be slightly different developement versions, different subcontractors, different batches of surface materials and such