Dave, I may be overlooking somethng as regards deformation of the disc holes when stored on a spindle in a storage container. But when the containers are upright, there is no pressure on the holes. If stored with the containers on their side there could be pressure, but, even then, only that caused from one disc's weight, and that is negligible in the scope of things. In a millenium, maybe. In a few years, no affect. In my opinion there is a greater chance of distortion from the strain imposed by the grasping ring on any jewel case, both as the disc rests in the case, and as it is being inserted or removed.
As regards the envelope paper scratching the playing surface. Sure, it's possible. In your case you may consider it an important factor due to a high number of disc removals. In my case, for my remaining years there may be as many as ten removals on some discs, no more, and for many only once or twice.
Thanks for your interest and I hope you get your problem resolved.