If I have 2 Super Munchkin or Half Breed (or any equivalent) cards, am I able to use up to 4 races/classes (Or 2 races/classes without any race/class related penalties)? Effectively, do these bonuses stack, or can you only ever have 2 races and 2 classes?
You can only have two.
Super Munchkin says:
You may have two Class cards...
Half Breed says:
You may have two Race cards...
So that's exactly what you can do: have two. It doesn't matter how many of them you have. All they say you can do is have two. They don't say "one additional" or "twice as many".