Hand Crossbows are the only core archery-type weapon that can be dual wielded by an ordinary PC race. Reloading becomes ridiculously difficult under these conditions (grafts for third arms, wands of unseen servant, and so on have seen use for this purpose), but it is... something. Kind of. My guess is that this, plus the general, ya know, “exotic-ness” of the weapons (see @Garan’s answer) seems to have caused it.
Do note that Hand Crossbow Focus (Drow of the Underdark) is effectively Exotic Weapon Proficiency (Hand Crossbow) and Weapon Focus (Hand Crossbow) in one feat. Also, Rogues get free proficiency for what that’s worth.
I doubt it was intentional, and certainly can’t be the reason for the initial designation of Hand Crossbows as Exotic, but with enough supplements, you can do some impressive things with them. With fairly considerable amounts of optimization, they may very well be the best ranged weapon in the game.
There are a lot of crossbow-specific feats, including several that add your Dexterity to your damage or half your Dexterity to damage. As I recall, it’s quite possible to get 2½ Dex to every shot, and since you’re dual wielding them (...somehow), you get a lot of attacks. Combine with splitting (which is an incredible special ability in general), and you’re looking at a number of attacks best described as “stupid.”
And then you could combine this with crit-fishing optimization, where you apply keen and aptitude to them, and use the Lightning Maces and Roundabout Kick feats with them. You are statistically way more likely to kill something than you are to run out of attacks with that set-up... not really recommended, but I have seen the combination used as an example of crossbow optimization before (I’ve also seen it done with a four-armed race that dual-wielded Great Crossbows, but that’s besides the point).