I'm not an expert in this, but I would imagine that tubed cigars are a marketing ploy. I haven't necessarily found them to be more expensive than cigars with or without a cellophane wrapper.

Case in point: different vitolas of the same cigar will be packaged in different ways. Take Partagas Black (Dominican Republic). Two robustos - the Clasico and the Crystal. The Clasico averages out to be only slightly less expensive than the Crystal. The Clasico ships in cellophane, the Crystal in a glass tube. Why? I have absolutely no idea. Maybe they think people will think they are getting a fancier cigar that way.

Glass tubes don't make a cigar any more luxurious, rare, better tasting, or desirable. There are many cigars that come in glass tubes that I probably wouldn't smoke (Macanudo Vintage 2000), wouldn't normally keep in stock (Camacho San Luis Y Martinez), or can't afford (La Aurora Preferido).

Again, unfamiliar with the intricacies of exactly how the corks work on glass-tubed cigars, what (if any) air gets to them, or what tubes do to benefit the cigar experience, I would say that if you are concerned about the glass tube having a negative effect on your tubed cigar, take them out of the tubes.

One more thought: ISOM's, Tatuaje, Illusione, and the higher-end Padrons and Ashton VSG/ESG's are not kept in any tubes or cellophane. I consider these cigars to be some of the finest around.