Wasn't BS Zelda (Combined patch) fixed in a previous fork posted here?
I seem to recall either @FateForWindows or @ramzinouri posting the fix for it, though I'm not sure who did said fix.
Here's one of the BS Zelda fixes I found from around that time, perhaps the fix for the combined patch (MottZilla's patch: https://bszelda.zeldalegends.net/rh.shtml) is in one of the commits from his GitHub, but it was never made as a PR to the main repo:
https://github.com/ramzinouri/snes9x_3ds/commit/37a1e328d206f9c300e1bced6a4c441dc078d886
Yup this BS Zelda fix is merged into the current Snes9x_3ds v1.20 release. A number of BS Zelda games work now when it didn't in the v1.11 and earlier versions.
What I said about not working in CIA mode (but is working when launched from HBL) is the New 3DS's ZL/ZR buttons.