I could be wrong, but I think that Bat-Mite is one of those things that is considered canon when he appears, but then when he's not around they just pretend he doesn't exist. There is actually a Bat-mite series currently running. He just met Damian Wayne (Robin) last issue. It's just one of those things that comic book universes can get away with, like having wolverine going around killing people in Uncanny X-Force, being a responsible teacher in Wolverine & The X-Men, and then being a complete joke in some random issue of another comic, and all of them are canon.