I ran into the same issues as described here. The following steps resolved my problems:
Step 1:
autoconfigure your joypads once by starting mupen53plus while having all controllers connected properly
Step 2: in
opt/retropie/configs/all/autoconfig.cfg -> Disable N64 Hotkey here (this was my biggest catch because it is in the all directory!)
Step 3: in
opt/retropie/configs/N64/mupen64plus.cfg -> assign the hotkeys and put the mode of all registered joypads from 2 to 0
After this it seems to work for me without any problems. So I hope it helps.
PS: I believe that the WIKI should be updated with Step 1, this is such a catch when trying to follow the WIKI N64 instructions.