Stubbed IOS'es are the programming equivalent of an empty box. It has all the characteristics of a normal IOS (name, version), but it simply contains no code that actually DOES anything.
Obviously, you're not going to run games from stubbed IOS'es (it's kinda like trying to drive a car without engine). But as syscheck shows, you'll have plenty of IOS'es. Games need a certain IOS to run (which one depends on the game...I only know by heart that the guitar games use IOS37), but backup loaders can usually force them to use a different IOS instead (even a custom IOS).
Programs like
DOP-mii are a good tool to tell which IOS you have, and probably to install previous versions as well.
However...having a stub isn't so bad as it might sound. syscheck told me I've got 8 of them stubs (IOS 4, 10, 11, 20, 30, 50, 51, 254). Yet I haven't had any problem with any game thus far (I simply don't have a game that uses it).