In case anyone stumbles across this thread and is looking for hope, here's how I found my folders on M1 mac!
From the PokeMMO launcher, click on Mod Management > Open Mods Folder
For me, this opens the following:
~/Library/Application Support/com.pokeemu.macos/pokemmo-client-live/data
Open this folder and it should contain your mods, themes, strings folders, etc. π