Is there a way to see what you're missing from the zoo?

I did upload my collection to SubetaLodge, but I don't know if it's working.

No, there isn't unfortunately. Subetalodge is probably your best bet for keeping track, or adding all the missing ones to a WL.

It's not really a collection like the others (plushies, beanbags) in that way - you can take things out, you can have duplicates, etc. So what you're "missing" can also be arbitrary and personal, unless you're trying to keep every minion ever, which is probably why it doesn't have a checklist.