I have done some research into this matter, seeing as how my Banknote Certification Service does not perforate their holders and hence, does not let them 'breath'. I have contacted some paper conservators and their answers are consistent - due to the high quality paper used in the making of paper money as well as the type of inert plastic used, air tight long term storage should not be an issue for generations to come.
Now I don't know much about the chemistry behind this; I'm a numismatist, not a chemist. However, I'm willing to take the word of someone who does this for a living. Believe me, I looked into this with serious trepidation. The last thing I want is an angry mob after me because my holder has destroyed their prize pieces.