Agreed, and every reference to Wonder Bat post-2005 probably was in some way, shape, or form inspired by DCAU. I can't imagine too many people would be citing the JLA run as why they love that pairing.
Also, I don't remember who released the idea of Wonder Bat for public consumption first, the DCAU or the JLA comics, so who knows if one source influenced the other, or vice-versa. Still, I'm of the opinion that DCAU would've gone in that direction whether or not Joe Kelly wrote it into his run.