The answer, I think, is found in the original purpose for the World of Greyhawk Fantasy Setting. It’s a game!
Greyhawk wasn’t published as a world-building exercise. It was not intended to be an experiment in scientifically and historically accurate game design. It was designed to accommodate the very specific needs of gamers playing the Advanced Dungeons and Dragons (1E) game system.
In that game system, there are two tensions at work. The first is the need for the players to have room in which to expand to play the famed “end game” of AD&D; clearing land, building keeps and towers, and eventually attracting settlers and taxing them. This, I think, is the reason that most of the small villages that are portrayed in the game are shown outside of the normal feudal system of government; who was ruling over Hommlet before Burne and Rufus decided to set up their fortress? By having hexes that are mostly empty, there is plenty of space for players to set themselves up as described in the DMG.
The second, I believe, is the need of the DM to not be overwhelmed by needless detail. Why are Hommlet and Nulb the only villages in their respective 30-mile-across hexes?
Because from the standpoint of the DM, that’s where all the action is! If there were a historically-accurate density of villages and farms on those hexes, the player characters would be overwhelmed with choice. “Which village with an inn is the one that we should concentrate on? Let’s pick this one! I think the name’s neat!” That requires the DM to then have exacting detail on all those villages or be willing and able to make up such detail on the fly.
Having a limited number of settlements from which to choose is the wilderness equivalent of a dungeon crawl. By limiting the players’ choices, the DM makes his own job infinitely easier.
Also, it is much more difficult to justify wandering wilderness monsters in a thickly settled location. There’s a bulette in that valley? Why haven’t the inhabitants of the three villages within 5 miles banded together to dispatch the nuisance? That question answers itself when those villages aren’t there.
Quite simply, having such isolated settlements might not be historically accurate, but they sure make the DM’s job easier.