would the Clan protectorate use protomechs?
No, only the Hell's Horses and the Snow Ravens use them in this era.
and would the Spirit Cat's have any mechs that were republic faction availability still around?
That's interesting question.
► On one hand, it's entirely acceptable that the Spirit Cats acquired some RAF 'Mechs in the chaos of those early years of the Dark Age. That's possible.
► On the other hand, after almost 15 years of combat, I think that many of those originally Republic-owned 'Mechs have been destroyed. However, it's possible that some more durable units (or 'Mechs and vehicles piloted simply by some lucky pilots) are still serviceable.
Plus, it has been a decade since the Fortress of the Republic cut off access to all core Republic factories. Thus, no access to new Republic 'Mechs and spare parts for them.
► My impression is that the Spirit Cats use mostly equipment of FWL and Sea Fox origin now, with some generic IS units - simply because that's what the new FWL has available. Yes, some Republic units, but only here and there.
► You may check these topics:
BattleMechs produced in the new FWLCombat Vehicles produced in the new FWLBattle Armor produced in the new FWLI mentioned some factories that were stolen by the Republic in 3080s and returned in 3130s. The Republic possibly retooled them to produce some modern 'Mechs and vehicles, but we don't know of what type.