In my very humble opinion, you should repair them. Without seeing pics, it's hard to tell but it will probably have more resale value if the seams are fixed.
I would:
(a) cut back a section
(b) make up a plate of steel
(c) put a 90 degree bend in it
(d) offer it up from behind
(e) plug weld it in
(f) continue until all of the rusted out seam is replaced
(g) grind the resultant replacement seam to an even level above the surrounding panel.
However, unless it is a rare shell it may not be worth repairing. It's a bit contentious, but from a safety point of view I tend to regard very badly rusted shells as a liability. I've given up on my Clubman van as the shell require more work that I was prepared to do given the best possible result.
I used to love the deseamed look, but now prefer the standard seams. If you deseam, you have to do both sides, and probably the front and back (Never do the roof! It looks awful IMHO) - a lot of work if only part of the seams are rooted.
Compare all this work with finding another shell and rebuilding, and consider the overall result in each case. Many projects are begun (by me!) with good intentions, and end up in the junkyard.
<edit> Mike's post slightly prempted mine and along the same lines. I repaired the rust in the rear roof seam with my method and it was pretty good in the end. Also easy to skim coat and paint. I like Mike's welding in of a plate across the rear of the seam too - will incorporate this into my workflow in the future
