I think it's something to do with the range which actor fade is set to on the xbox. Maybe they didn't want people shooting farther than they can see and hitting something, and when they ported Skyrim to the PC they didn't mix the arrow range to actor fade?
I guess they may eventually do something with this in a title update, but why even bother having a zoom perk on the Xbox based on that statement? Even though the Xbox draw distance is significantly smaller than the PC version, the zoom perk increases that distance. If I can't hit a stationary object that I can see while using Eagle Eye, then how can it not be a bug? This is clearly not expected - you don't build a scope mechanic for a weapon in a game that requires shooting enemies (using that scope) if you do not want them to be hit at a distance where they can only be seen through the scope. I saw some posters comment on this problem for the PC with FO3, but I never had trouble with my Liberty Rifle sniping through the scope on the 360. I am sure test saw this problem and Bethesda is likely already considering addressing it, along with the grab bag of other buggy/glitchy corrections that need to be made.
Since it is clearly an error on the Xbox version...which the 'port' to PC came from, how can the PC version be perfectly fine? Mixed results can be accounted for because of mixed PC hardware/software/driver combinations. Just because someone can hit one guard at Whiterun repeatably doesn't mean that the game is not bugged. All sorts of bugs occurs when some mixture of the PC components cause problems; hence the difficulty in coding PC games and subsequent attractiveness of console based game development! Developers have to account for a million variables, especially when end users can tweak so many numerous video settings for their own playthrough.
On the Xbox version (I realize this is a PC thread but I am making a point) - I can seen enemies just fine when I zoom in, I'm not even very far away from them (maybe 70 yards, hard to tell without a way to determine the GU distance) but the arrows just go right through them. This was never a problem with my skill 100 archer in Oblivion, I just cranked the aim reticle up enough and I could hit anything that I zoomed in on. (Normally accompanied by a devestating poison that would result in the poor bastich daedra dying before they could reach me!!

) Now, with Skyrim's new engine - non-agressive wild game, mammoths, giants... just can't be hit at zoom range. I haven't found too many bandit camps from a distance since I gained Eagle Eye to try and test the usefulness of the perk on those enemies. It is easy to see that shooting the bow lends an odd arc to the arrow depending on the distance of the enemy. (Even though I'm pointing straight at them, the arrow trajectory arches upwards more on release as the distance between myself and the target grows) I would much rather just turn that crap off, with a toggle for those who need it. I much prefer the realism of accounting for distance myself, especially if that is causing some odd arrow physics behavior.
I feel certain that the Navmesh .ini change will be a part of the solution towards balancing archery results against all Actors, but will be a long time coming for anyone not using a PC.