Sorry for being late to the party, but, IMO, this doesn't sound like
a right approach to the problem of invisible emphasis markers. A user
choosing to hide emphasis markers should not need to—or even be given
the opportunity to—display them in order to edit them efficiently.
I agree that if org-emphasize handled marker visibility states in a DWIM fashion, then a user should not need to display them, but why do you believe they shouldn't have the opportunity, especially given that this is the exact behavior of prettify-symbols-mode?
Could you walk me through, in your proposed DWIM system, how a user should be able to remove or change emphasis markers after they are rendered and hidden?
Shankar