There are certainly several things that should be considered when overclocking, but to add a few things here:Be aware also that with some weapons Overclocking seignifically reduce the time a weapon can constantly fire: this maybe not a problem for a dogfighter when you'll have a limited time-on-target, but when dealing with larger and more resialint ships tath could be a withrow instead of an advantage: remember S3 shield and above constantly regenerate.
1) Not every weapon overheats. At least I've never managed to get my ballistic scatterguns to overheat.
2) Some weapons overheat but instantly recover, like ballistic gatling guns.
(Oh, could also depend on size, haven't tested everything)
And then about S3s (AND S2s with the exception of Sukoran) constantly regenerating, well, that could also be the reason you NEED to overclock your guns.
Say you happen upon a Starfarer Gemini that has just one S3, but it's FR-86 overclocked. That's 6772 hp/s regen. It's just 20k hp per shield face, but if you're not doing over 6772 dps, you should just give up.
With most ships, you'll need a very specific loadout and overclocked guns to overcome that, like for Freelancer I think the only option would be overclocked predators. (And since they're ballistics you can get it destroyed even without getting the shields down. Still, those are scatterguns so you'd need to be right in the face of that ship). Putting all your missiles on it might work (as long as counter measures don't eat any), but they'd need to be Thunderbolt IIIs, smaller missiles you'd have more total damage, but since you can only shoot 4 at a time you'd once again need to overcome that regen.
If you got a turret gunner, that makes it easier but still.
HH with two FR-86s overclocked would require like a dedicated bomber or something to take down. (Luckily the NPCs are dumb, so you won't be encountering such monster in missions afaik)