So, you know how if you Accept Payment on a customer and the only applied to transactions are offsetting journals, how there will be a $0 "payment" created with no actual record? Is there nothing that can be exposed on the JEs to indicate this has happened? If you edit, you get a warning that payment(s) can become unapplied but I'd like to be able to search for Journals where these phantom payments have been applied (or were and then become unapplied).

I don't think you can find them if they have become unapplied, but you can search for them while they still are applied. Use the "applying to" or "applied to" fields on the transaction search.