Actually, the codes shown as “deposit address”, which can be scanned via QR, are not meaningless. They are exactly the code that you can use as an admin in the deposit tool. The code uniquely identifies the combination of user and currency. It is meant to be used for any other type of deposit, as long as you can verify manually that the deposit occurred. Therefore they are shown as intended.
What you suggest could be added as an option: if it is checked, then the deposit address for custom coins can be hidden from the JSON API, and therefore will not be shown. And it is possible to change the deposit dropdown to not show any coins without a deposit address. This would require changes both in the parent plugin and the coin adapter.
I will plan to roll out the necessary changes with the next releases for these two components.