JONNY QUEST made sense because usually Race and Dr. Quest weren't usually looking for trouble. Now, if Race and Dr. Quest were crimefighters or spies, you'd better believe Jonny and Hadji wouldn't come along.
I just watched an old tape of this wherein the gang receives a distress call from a scientist who has created some kind of rampaging antimatter monster on a desert isle. Dr Q piles them all into the plane without a second thought and then uses the kids to spring a trap on the thing inside a cave!
If the superpets were overused how do we describe the extended use made of most of the central conceits of the classic Superman --the ubiquity of Kryptonite, Clark and Lois' identity politics games, Lex Luthor's multiple escapes (sometimes twice in one issue), etc. If their humour is intrusive, how do we characterize most issues of Lois Lane or Jimmy comics? Not to mention most of the 40s and 50s? Susie T, J. Wilbur, Mxy, Toyman, and later Bizarro, etc. The hypothetical line that is crossed in your Luthor/Krypto example (or Darkseid/Super Monkey) doesn't really exist in Superman (let alone Capt Marvel).