It is incredibly likely that the reason which "Wednesday is Missing" cannot be released on the (Almost) Complete Collection of The New Scooby-Doo Movies is John Astin.
Though Hanna-Barbera was able to release their 1970s cartoon version of The Addams Family on DVD, this version did not include John Astin and Carolyn Jones as the voices of Gomez and Morticia, respectively. "Wednesday is Missing" was the final time Jones would ever provide Morticia's voice. However, John Astin returned to voice Gomez in a 1990s cartoon adaption of The Addams Family, which HB has also been unable to release.
~ WildwindVampire ~