The OP is clearly already using a Humidor (as stated in the original post).

I am assuming that it really doesn't matter if the cigar is in the tube or not as the humidity should be the same inside and outside of the tube if it sits in the humidor more than a few days.

What kind of tubes are these? The simple thin metal ones with the screw cap or something more fancy? Most tubes are hardly better than cellophane at holding humidity.

I don't know much on the subject though as I only have 2 tubed cigars in my humidor. I'm curious to see if there is a better answer out there.