Using a hand crossbow is simpler and easier than using a light/heavy crossbow, isn't? So out of what considerations is Hand Crossbow regarded as Exotic Weapon in 3.5e?
In 4e, Hand Crossbow is categorized into Simple Weapon, that imo is more reasonable.
This is mostly based on a lot of the lore present in 3.5. I believe it was designed to incorporate mostly Forgotten Realms (as many of the canon gods and people are in both), but I could be wrong.
But this rule is probably based on Forgotten Realms. In that setting, the hand crossbow is a weapon designed and used almost exclusively by the Drow (dark elves). Therefore they may have decided to keep that idea. Look at the entry in the Monster Manual for Drow and you'll see they use the hand crossbow.
It may also be a matter of how it fires. The recoil from that might be hard to control with only one hand.
(I also can't help but think of the Cleric Quintet by R.A. Salvatore, in which someone builds a hand crossbow based on a picture of one, and there are times when people are actually surprised to see a human using one instead of a Drow. The Legend of Drizz't also makes many references to it being a popular tactic of the Drow to fire a single poisoned shot with it before engaging in melee).
A non-D&D related answer, based just on real world mechanics:
A crossbow is fired from the shoulder, like most modern rifles, and you can aim pretty well with it.
A hand crossbow, and especially a wrist-mounted crossbow cannot be aimed well, especially without training. Being proficient with a common crossbow will not help you here.
Weapon proficiency in D&D means that you can efficiently use the weapon. Someone without any skill in longswords might pick one up and swing it in the general direction of the enemy just as it were a stick, but will most probably not achieve anything, so in game terms it is simplified to not being able to equip it.
Now imagine a weapon which is very uncommon, and with which you cannot hit the broad side of a barn from a few steps if you are unfamiliar with it.
Edit:
Loading a hand crossbow would also be a challenge for a normal human (this is probably why they did not see widespread usage in real life). Remember, that with a bow or crossbow, the force you inflict upon your enemy solely comes from the force you used to draw it. You don't only want to touch your opponent, you want your arrow/bolt to pierce armor, clothing, skin, and still do enough tissue damage to do harm. With a bow, you hold one arm straight, and use the full force of your other arm to draw the bow. your arrow will hit as hard as much force you can draw the bow with. With a crossbow, you put one foot in the "stirrup" at the end, and you can draw the string upwards with both arms and your back muscles. This is why a crossbow hits so much stronger than a bow. Now look at a depiction of a pistol-sized crossbow. How do you exert enough force on it to store enough elastic energy in the string? You either have to have superhuman strength, or possess some techniques which I cannot imagine, to load your hand crossbow. Those small pistol-crossbows you can see on Youtube might be useful to hunt small birds, but they don't have enough power against human-sized targets to be of any use in battle.
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).
My guess is that hand crossbows are simply rarer weapons. Going on the assumption that Dungeons and Dragons pulls from medieval history (especially from the wargaming angle) than the types of weaponry the game has will be influenced as such. Standard two handed crossbows seem to be the ranged weapon of choice until being replaced by firearms. A smaller shorter ranged version would have less utility then the two handed version because it has less range and is probably more difficult to manufacture (seeing as miniaturization is usually a sign of more advanced weaponry). Sheer lack of commonality could have been a qualifying reason as to why the weapon was classified as exotic.
This also ties in with who the weapon is going to be used by: simple soldiers or highly trained assassins and thieves. It themes better to have it exotic.
Perhaps they thought it would take more skill only using 1 hand. In RL some smaller arms are harder to shoot with accuracy than rifles.
