imho and the opinion of Sony (for one example) for any ENG (not cinema) format, camera cards are an acquisition format, not an archival format. Rewrap (not transcode unless you want) out of XDCAM, P2, etc asap. There’s no good reason to keep the cards intact and many good ones to not. CatDV (and other software) can extract the metadata and keep it with the new rewrapped mp4, mxf, or mov files.
As to cinema cards, this is one I can’t really comment on due to the fact that I’ve never been hired to work on them. But I will say, as you know, the major film archives are storing dpx sequences. Not sure if they are converting RED and similar to dpx for this (sources) but masters are done this way.
I’m personally outraged that the camera companies made these formats with little to no thought given to the archiving of these cards and media. They dropped a huge issue into the laps of shooters and content owners and took the money and ran.
I hope someone can manage to answer this in the next round of formats.
As to the data model, in CatDV, for example, this is accomplished by recording the “card” as an object and then clips underneath it. This is a relatively simple relationship, but it works fine. I’d assume that this idea is as old as a reel of film that can contain several scenes and your archival friends will show you how this is done in “real” archives. (Post people never get to seriously archive at a level of say a film librarian or someone from one of the studios.) I’m teasing of course but as you know, when you get to the true high end of the business, post and archive are often separate departments and post is simply delivering to the archive team.
Hope this helps and I hope smarter people than I post up as well!