Hi Jawhn!
The CPU's I believe are another custom Nintendo product, "RP2A03". They can't be burnt, but they're the same on every vs. game and board. So if you already have one you could switch it out, or if you found a bad board with a good cpu chip on it you could steal it off of it. They're all socketed and easily removed.
The reason many of my boards don't have them is because you remove them sometimes to put a daughtercard on... so many of these boards have had daughtercards installed and either lost the cpu chip or it's on the daughtercard still!
I guess the way they originally came was that the daughtercards didn't have cpu's on them, but over the years people just left them installed in there.
I think you can pick the cpu's up for $5 or so, but you'd have to find somebody that has some. I think I heard Mike's Arcade carries them?
Edit: I just checked and he has them, but wants $25 each! Apparently you can also get them off playchoice boards, punch out boards, or DK3 boards as well as all the vs. boards.