It's more like:

Cruisers > Destroyers > Frigates > Corvettes > Fighters > Bombers > Cruisers

That's the basic gist of how different ship classes interact in Homeworld, but each ship class also has its variants that make them better/worse against other classes. Some are best at doing what you expect, like multi-gun corvettes against interceptors, but others can also "punch up" somewhat like Ion Frigates versus Destroyers or Heavy Corvettes versus Assault Frigates.

A good example of a ship that subverts the standard formula is the Missile Destroyer. You assume they'd crumple under bomber wings like any big dumb ship, but anything less than enough bombers to destroy a small moon in one pass will get decimated because a Missile Destroyer is designed to be an anti-strike craft vessel. Scouts on the other hand can keep it tied up for a while, since they're fast enough to evade ze missiles.

So the whole "rock-paper-scissors thing" isn't quite so rigid and this is probably what's making confusing for you. It's not so much "rock-paper-scissors-shotgun-nuke" as you put it, more "one of your rocks has a sharp pointy bit that can pierce thin paper" or "one of your pairs of scissors has thick metal handles sturdy enough to crack a pebble with." Now all the bombers in the universe still won't destroy a wing of scouts and no amount of ion frigates will stop a bomber armada, but you've got a bit more leeway than you might think.

A lot of it comes down to judging your ships' weapons, armour and speed against the enemy ships' weapons, armour and speed, and choosing accordingly. A wing of scouts will last for ages against a heavy cruiser because they're nimble enough to avoid it's slow-arse mass drivers, but don't expect them to do much more than scratch its paintwork. Bombers would be best since although they're slower than scouts, they're still fast enough to avoid the cruiser's guns and pack a decent punch. A single Destroyer will last about as long as an ice cube in a supernova.

The only other thing I can suggest is to just play through the campaign and try to get a feel for how it all fits together. Maybe even try a couple of skirmishes against the CPU on easy, or mess around in multiplayer with a friend experimenting with different ship compositions (bombers vs assault frigates, interceptors vs heavy cruisers). Experience really is the best teacher when it comes to Homeworld.

I am in no way a expert like a lot of people here, but I hope this helps make it a little less overwhelming for you.