Try going to Business Framing Issues and read earlier posts on Matboard Storage. You may find it worth reading.
I asked the same basic question and got some good response out of it.
These guys are great on here.
I have not been putting anything between regular glass and it has been fine so far. (no scratches) But the Conservation Glass I leave the paper that comes in the box between any pieces I am storing. So far, that has been fine as well.
Here I go again, showing off with my homemade tables!
This is an old photo from my first location prior to buying my last building in 1995 but the table is the same one I use today.
This was back when Premium Clear was my default glass of choice. It is surprising how tastes have changed with the move. Now I only offer Conservation Clear and keep only a smattering of regular and reflection control around for the few that insist on them.
The slots will handle all sizes up to and including 32x40 glass boxes. I stocked alot of sizes back then but now I keep mostly 24x36, 32x40, and 36x48 in Conservation Clear. I can cut most of what I need out of those sizes.
I leave the glass in the boxes as they have interleaving between the lites and it serves no purpose to take them out until I need to cut a size for a job.
I sell mostly all glare flavored Conservation glass. I have very little call for Reflection Control glass and don't stock but one box of 32x40 just in case someone asks for it.
I am right on the Gulf coast and the intensity of the sun here seems to be much greater than anywhere else that I have hung my hat over the years. So I push CC glass strongly and would advise others to do the same.
Glass is probably the least expensive of the visible materials used in a framing package and it isn't the place to take shortcuts to get the price down for a customer, in my opinion.