I have the same issue with my 2004 Acura MDX (not surprising, since it’s a close relative of the current Honda Odyssey). In the MDX’s case it’s a little bit better because it has automatic headlights, so you can leave the headlights in the "Auto" position and they’ll go on when the light sensor on the windshield detects that it’s dark outside. (The same sensor is used to control the windshield wiper’s automatic setting.)
However, I’ve found that the sensor isn’t sufficiently sensitive, i.e. it doesn’t turn on in dusk when I would choose to turn my headlights on manually, and it won’t turn the headlights on in a heavy rain during the day. This is especially problematic as I’ve heard that there are now U.S. states that mandate having your headlights on whenever your wipers are running at full speed.
I happen to have a BMW with an automatic light/rain sensor and it’s much better than the Acura at deciding when to turn the headlights on, esp. in the above situations.
If Honda offered Daytime Running Lights on their cars in the U.S., this would be less of an issue, but for some reason they don’t even though nearly identical models are sold in Canada with DRLs.
In any event, the nav system’s automatic behavior should be determined from the ambient light in the car, not whether the headlights are on.
Adam, you should let me know if you figure out the registry setting in your car to fix this.