Entirely possible that the car did not have them "installed" from the factory but came in the glove box for the owner to install.
Just read an article/interview about the origination of the Roadrunner in the August 2014 MoPar Muscle magazine. The interview was with the original Program Manager of the Roadrunner, Jack Smith. It's a great article, but the section pertinent to this subject reads as follows:
"Not everyone in the notoriously conservative company [Plymouth] was enthused about the idea. Dick Macadam, then Chrysler-Plymouth's styling director, wasn't having any part of it, emphatically telling Robert Anderson in an impromptu hallway meeting: "Nobody, but nobody will ever put a cartoon bird on one of my cars." according to Jack Smith. In order to provide decal maker 3M, a Chrysler part number in time for production, Jack suggested to Macadam and Anderson the idea of having the bird decals come packaged in the glove box, with instructions telling owners how to install them. Macadam reluctantly agreed to this-as long as he could pick the particular image to be used on the decals." The article then goes on to state that at a 68 model preview at the Highland Park headquarters the decal was installed on a pre-production Roadrunner being shown to a group of Plymouth dealers and they loved it. The decision was made at that time to put the decals on at the factory and not include them in the glove box.
However, word traveled slow back then and all production facilities may not have received the directive to install them before some cars snuck out of the factories.It could be assumed that being a very early production car, that this reference was being seen as fact and that through common knowledge, early cars may not have had the "Birds" installed at the factory and that some dealers/owners might have never put them on the cars. All of that being said, I wouldn't believe there to be a "decal delete code", it was simply practice.