Firepower and slots sizes were a major factor, as per your specific examples:
“Frigates Class - Half of them are labelled Cruisers in their name, in fact there's more cruisers than Frigates. ”
There's no cruiser class. Most of the ships that are "cruiser" are more or less glorified patrol corvettes with only moderate firepower. Not quite strong/big enough to really be a capital.
“Gunboats - 3 of the ships in gunboats don't make any sense, the Saboath, Alpha Starwing and the Starsaber MKII ”
The Alpha Starwing is in fact commonly called/known as the assault gunboat or cygnus gunboat, due to its weapon fitout, and should likely later be made to have a bit more hull/survivability. The Saboath will likely be moved, I had originally thought they had more HP than they did.
Per the JM5K, I've mentioned in half a dozen threads that due to the long process of making categories actually work, a couple of the fighter/light freighter/gunboat were in the wrong spots. Without looking, that's likely one of them.
YV-666, SWC has retconned the YV-666 to be a small capital ship rather than a Light Freighter.
Tabder, I originally had it in the Super Class, since it's a a "Super" RM Transport, but I was bitched at by like, everyone, so it was moved.