They are painted on glass? Or they are photos on glass?
If they are photos, they are called ambrotypes and will be very high quality photos. Scanning them won't harm them at all, and we see many scans of ambrotypes here on Rootschat.
If they are painted, I wouldn't think they'd be harmed either...but I really don't know. Prue (our moderator, and a professional conservator) would be the one to ask. I believe she is on vacation at the moment but you could always PM anyway.
Cheers,
China