Even a 5,000 copy run is still a very low number. Future potential as to going up in value is, as always, dependant upon the game itself and how well it is received by players. There are no doubt lots of games out there now that were absolutely terrible budget releases with fairly low, for their time, production runs and are pretty much under the radar and easy to obtain because they were generally very crappy games.
LRG's Approach is to offer true limited physical editions of games that have undergone tight quality control. This is actually pretty simple when you consider that every, or nearly every, game they have released and announced they will be publishing was already released asa digital only title. All the suckers who bought digital only in these cases did those of us who prefer physical copies the great favor of unknowingly conducting widespread beta testing so that the likely final version released on game cart will be a finely polished, hopefully bug free, edition of the game title.
I believe the only game they presently have announced as an upcoming title they will be publishing that isn't out yet in some etheral form or another is
Cosmic Star Heroine, but the developers of that game do seem highly passionate about the project and have been conducting testing on the game as they go along, so hopefully there won't be any issues in the physical release version that will be serious enough to warrant patching.