I’d say out of all the factions, Magmar has the strongest control, which makes sense since most of its stronger cards are 4+ while other factions have hefty 2-3 drops. It’s pretty slow outside of Starhorn, which is considered to be overall weaker than Vaath anyways, especially after the burn/draw cards from the latest expansion eventually get nerfed. The question you ask is a bit weird, since no board clear is the same between factions. I feel bad for Vet in general, but I think that might be partially because I’m a Magmar player and that matchup is an EZ win.
I wouldn’t call Yu-Gi-Oh the pinnacle of balanced card games, and certainly not a standard to compare to. To be fair though, if you didn’t have a counterspell card by the time the opponent felt it necessary to use black hole, you kinda deserved it.
If board clear didn’t exist, other means would be created to deal with aggro, such as powerful provoke minions that are immune to spells or something. The point is there has to be something to keep aggro in line, and board clear has been one of those answers since essentially the dawn of CCG’s.