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.
Not sure why it didn't move. I'll relook at the few that are wrong in light/gunship/fighters later this week after I play catchup with school. Been sick/working for the past 5 days, with next to no sleep, so I'm a bit behind.