No, no, no... Do Not remove IOS'es even if they are stubbed.
The only stubs you should ever need to remove are those in slots you wish to use (like 249, 250, 222, 223, 224, 202, 254)
DOP-Mii sometimes tells you that custom IOS'es are stubs too, so be sure that you don't delete the ones you use.
Waninkoko's cIOS'es install as: 249, 250
Hermes cIOS'es install to slots: 202, 222, 223
Bootmii IOS is in slot 254.
If you have Installed a patched IOS36 with Fakesign, and NAND permissions patch that's usually enough.
It all depends on what you're trying to do...