I would think that there may be an issue of scratches over time, dust tend to get into everything, moving the negatives around and stacking them on each other may induce scratches.....at least that's my initial thoughts, I may be wrong though, scratches may as well occur when inserting and removing the single negatives from the sleeves as well.

I like to have one strip per sleeve, much easier to find stuff, I also make a contact sheet, representing the sleeve-page and I store that along with the negative sleeve, so I can very easily find the exact negative to print (I also mark the frames I print on the contact sheet).