It varies by the launcher and role. For most rocket launchers, I'd assume that the entire system gets reloaded at once. For AFMs, the smaller ones probably also get reloaded at once. They carry enough for a single volley. The Unguided Rockets might be a bit different in that they reload half at once, since they have no designated 'volley' and more provide sustained damage.
For the larger AFMs (FRAG, possibly the Barracuda PRX) they could get reloaded a single fire cycle at a time (2 missiles for the Barracuda PRX, 1 for the FRAG missile) since you generally fire a single cycle at a group of fighters. Capacity is probably low for them.
For the general larger missiles (Hornet, Barracuda, Devilfish, Hunter, any others I'm missing), it probably depends on the role in that faction's navy. For the ISA, missiles are a major source of damage, I'd be fine with seeing lowish capacity, fast reloads. For the RSF (Hornet), I could see a high capacity, long reload, just like all the RSF ballistics. I'm not exactly clear on the UIN's position on missiles, but since they turn fights into slugfests due to the Fortress Shields and relatively ineffective weapons, I can see them reloading a few missiles at a time, low capacity, fast reloads.
For the smaller general missiles (Micro, Piranha, Eel, etc), I look at them more as support, when an enemy overloads you unload your missile racks. Therefore, they would reload their entire rack, since you unload the entire rack.
That leaves the Mosquito, which is the only Kinetic missile. It probably falls under the RSF plan of high capacity, long reload.
As for Torpedoes, I don't think I've ever used them over rockets. Larger torpedoes are just less useful than other larger systems, despite doing more damage. Torpedoes don't offer enough damage for me to give up the flexibility offered by other missile/rocket options.
In general, the ISA should probably have fast-ish reloads, since they rely on the missiles for damage. The UIN would probably also go with a fast reload, along with low capacity. The RSF would have high capacity, long reloads like their ballistic weapons. XLE only really have the Micro-missiles, otherwise they use rockets. So they reload their entire magazine at a moderate pace, I suppose.