While I was working as a cartographer at the American Geographical Society, then located on upper Broadway, a long neglected crate of glass negatives were discovered of pictures of the uniting of the transcontinental railroad. They were cleaned, printed and made into a book published by AGS. Storage was very much as in your case. Since glass is not very flexible, cracking of glass is a hazard. As I remember, some of the AGS plates were cracked. As for how to clean, I would contact people who do such restoration at a large museum.