The only time you have to worry about stub IOS actually breaking anything is if you're upgrading a system menu IOS. System menu IOS aren't used for games ever, so there is never any reason to update them. Likewise if you're just updating an IOS a game uses, you have no chance to brick your system menu... assuming of course you're installing the right IOS
The only IOS's that you really need to be cautious with are: IOS9, IOS11, IOS20, IOS30, IOS40, IOS50, IOS60, IOS70, and IOS80. This, however, doesn't mean that you should just go around messing with IOS's without knowing what you're doing.
The only time you have to worry about stub IOS actually breaking anything is if you're upgrading a system menu IOS. System menu IOS aren't used for games ever, so there is never any reason to update them. Likewise if you're just updating an IOS a game uses, you have no chance to brick your system menu... assuming of course you're installing the right IOS