You're very welcome!
Harpoons are my go to medium range "finisher" missile because it can safely fly over allies and deals good damage to armor and hull. They can travel a good distance and are very fast with the ECCM hullmod. They rely on other weapons to get the enemy ship in a good position to get killed, but then they do the killing.
Atropos are shorter range but better tracking harpoons, basically. A bit better per shot damage, a bit worse total damage per OP spent.
Sabots are very powerful anti-shield missiles, great for giving finisher's the opportunity to get the kill. They are a bit shorter range than Harpoons, so while they fly over allies in theory, a launching ship usually needs to be on the frontlines for them to work. They make for decent "panic" missiles because they will spike up the enemy's flux and make them back off.
Reaper torpedos offer tons of damage and are either very cheap (for the smalls) or have lots of ammo (for the mediums) compared to harpoons, but they don't fly over allies and are somewhat slow: frontline ships only and not effective vs very nimble (frigate) targets, but they can kill enemy big ships extremely quickly.
Hammers are like reapers but moderately faster, have much less damage per shot, and moderately less damage per OP. Sometimes it can be nice to have more smaller torpedoes instead of a single big one, but I usually prefer Reapers. Dual Hammers are not bad substitutes if reapers are unavailable and you want torpedoes though.
As some example builds: for my frontline Enforcers with officers and mid range guns, I have 2 sabots and 2 reapers. The sabots are in their own group and in linked firemode (so a single "mouse click" from either the AI or the player fires both), and the reapers are also in their own group and linked. They do waste more shots by having them linked because of overkill, but they get a lot more overloads and kills which I consider worth it. For my non-officered Enforcers with long range guns I go 4 harpoons.
For the AI using weapon groups: They handle them the same way a player would! The AI will turn groups' sutofire on and off depending on flux, and use one group as a "manual" fire (that single manual selected group is the only logic for testing firing vs enemy defenses, IIRC). They handle the auto fire settings themselves in battle, so that tick box does nothing for the AI. The 'linked' vs 'alternating' however does cause changes, especially for missiles, because in linked mode all the missiles in the group will fire at once. You can also do some nasty tricks like putting missiles in the same group as guns and linking them, so that whatever target makes the guns fire also makes the missiles fire...