Perhaps the Linc had fallen into a serious state of deterioration due to decades of neglect, but collectors would certainly want the patina intact. One would want to sit on the original leather the Kennedys were seated upon and view the exact interior surroundings present in 1962. The error of improper storage cannot be undone by a restoration.
As it is now, it seems the VIN plate is the only thing left from that fateful day, and that doesn't bring the big bucks at auction. I guess it can still be displayed somewhere as a novelty, but the collector value is slashed.
Imagine if someone refinished JFK's wicker rocking chair because he wore the varnish thin on the arms while signing bills. That'd be a collector sin alone, but this is like replacing the arms altogether and recaning the seat because some idiot stored it outside. Sure, it's still technically the Kennedy chair, but only a percentage of it. Value is depreciated exponentially.
They'll be lucky to see reserve for such a relatively insignificant automobile.