UPDATE: Tried the other app mentioned in this thread, for me JoyToKey has been working very well in this setup and would be my recommendation if you are using these sticks (you are going to have trouble in various emulators).
If I were starting this build again, I would probably hardware mod at least one of the sticks to use a different controller board (fightstick PCB or cheap controller from amazon, i-pac, whatever), assuming I don't mind changing the original hardware. They are a great feeling fightstick but detection is hit and miss across different emulators / OS / frontends since they were only really ever designed to be used with the Neo Geo X. Doing the hardware mod would allow them to work as a pair on the raspberry Pi I suspect, so in that case it might be the only viable option.