Yes, at least if you count pirated games (which are neither licensed from Nintendo nor from whomever owns the game, so twice as unlicensed). Per this moment in a REcon presentation on the Nintendo 64 CIC:
... now I should say, unlike the older Nintendo stuff, instead of having very widespread pirate chips, this pirate game is actually very very very rare. If you actually have one of these and you're willing to donate in the name of science we'd actually really like to see what's inside those. There's a very small number of pirate games made in Hong Kong that have this chip and we have very little information about the history of this pirated CIC. So, again, please let us know if you have any leads on these.
Since the presentation is an in-depth look at the Nintendo 64 copy protection by people who have studied the thing at length, and that appears to be the only reference to illegitimate copy protection chips, it's probably correct to say that there were no unlicensed games with original content, and very few pirated games. Nintendo's approach in the 64 was sufficient in practice.