How to track down message notification?

Does GB itself detect SMS and notify, and because I've enabled notifications from my SMS app I'm getting both?

Yes, I believe it does...

To track it down for sure, probably the best bet is in Gadgetbridge soon after you got an SMS, click on Debug then Fetch device Debug Logs

Connect your phone to a PC and set it to share storage, then look at the log file in Internal shared storage/Android/data/com.espruino.gadgetbridge.banglejs/files

In it you'll see some lines like SENDING GB({"t":"notify",...

And you should be able to see in those lines if you get two similar ones I think they'll have different src values that might help track down where they're coming from