Not in pve, but in pvp i've heard gun shots before and known someone was around. Arrows are a little quieter. This is pretty much a non factor for high level weapon choice though for hunters....they'll definately take a gun if its good.
PvE - no, noise makes no difference on mobs and guns are usually a tad higher DPS than a bow of same level. PvP - bows are prefered as the noise is fairly quiet and harder to locate. And even though the name might imply it the gun Silencer is in fact not silent. Heh, be cool though if engineers could tinker up silencers for guns but can't have everything.