I had several projects that I recorded maybe a decade ago with Pro Audio 9, and I saved them all as bundle files on disk. I opened one with Sonar 2 a few years ago, but now the same bundle is missing audio files when I try to open it with Pro 9. In fact, all of the bundles I saved are missing audio. Is this normal disk data deterioration, or is something else wrong?

Unfortunately the Bundle files are proven to be somewhat vulnerable. If they get corrupted, there's little to do, AFAIK.
My guess is, you've lost the data, unless, for some mysterious reason, trying several times would get them opened.
Sorry.