Reload times are the same for all ranged weapons. So I'm guessing Toady calibrated the reload time to that of a crossbow, which was the only ranged weapon that dwarves could use. And it certainly does take a long time to reload an old style manual crossbow if you don't know what you are doing. Hell it takes a long time to reload one if you DO know what yer doing.
At any rate if you get really high skill with your weapon you will see a significantly shorter reload speed. At legendary you basically don't have a reload delay. It's like you modified your bow with a magazine or something. It just takes a bit to get there.
And throwing rocks trains archery skill because archery skill just seems to be your ability to judge the target's distance, lead the target properly, and things like that that make you better at hitting a target at range regardless of weapon. It's just like how fighter skill increases your melee combat capabilities regardless of weapon.
But as stated, yea, throwing a bolt is just about as effective as firing one from a crossbow. There do seem to be some mechanics in place to make firing it from the proper weapon be better, but those are either bugged or too insignificant to matter. Throwing a ballista arrow or trap component is also remarkably effective if you can get your hands on one. Though they don't retain their ability to multihit from fortress mode, nothing quite yells awesome like a thrown serrated disk slicing somebody clean in half.