Yes, JPG's are lossy, but everything is scanned at 300dpi - storing the images as anything else would just be silly.
Also, PDF is not "really" proprietry anymore - the specs are well known. However, even if we were not to use it - what is the alternative that is not multiple files? I don't know. Hence the poll!
You are right of course. I should have mentioned that on low colour scans, PNG will be used.
Have a look at the website in my sig.