to get Fullscreen, just hit x or m when launching a Rom and Change your Resolution.
Or do sudo nano /etc/emulationstation/es_systems.cfg
Press Cntrl+w and search for “Nintendo 64”. Then Change runcommand.sh 1 to runcommand.sh 2.
This changes your Settings to start your games in the Default Resolution (so 4:3 and not stretched to 16:9).