Hmmm, I still have my N64, all my old games, etc and could test. Do you know if there is a way for me to check the memorypak to see what games actually saved to it?
Now that you mention it, I recall either OoT or MM saving to the cart directly.
Edit: May have found my own answer:
HOLD THE START BUTTON DOWN and turn your console on. Make sure to HOLD THE START BUTTON DOWN while it boots up. This will pull up the data management screen where you can view and delete your stored data on your memory card.