Nomads aren't given a rep (in Vanilla atleast) to stop players from continually shooting them and becoming friendly with every faction in the game. This has potential to really effect server balance as everybody would just shoot Nomads and in turn render all other NPC's useless.
As for Zoners, they are infact slightly effected by the Xenos, IMG, GMG, LWB, BHG, Lane Hackers, The Order and Unioners. But these are all Positive bonuses, so you have to become friendly with those factions and you'll get a very minor boost to your Zoner rep.
