I don't think there should be any music issues at all. From what I've read, the songs performed by the Splits were original songs specifically written, produced and recorded for the show. Yes, some sort of compensation would be required for the song writers and performers on the songs, but as far as I know, the songs themselves are owned outright by Hanna-Barbera.
Looking at both the Deca album and the Kellogg's singles (I have the album and both singles), all are copyrighted by Hanna-Barbera. They all also say (and this is most directly related to the actual songs themselves) A Past, Present and Future Production by David Mook for Hanna-Barbera Productions, Inc.
The credit on the third and last Decca single ("Love To Love"/"Pretty Painted Carousel") is slightly different. This is from memory but IIRC it still says "A Past, Present And Future Production" but the actual producer credit says Aaron Schroeder (or possibly Schroeder and Mook). I have a promo copy that says "stereo" on the label but is actually mono. Initial copies of the We're The Banana Splits album did not carry a copyright notice at all (it was omitted in error) but a copyright for Hanna-Barbera was added to the second pressing front cover. There are many copies out there with the copyright notice added on a sticker. But this album is from 1968, and prior to 1972, the copyright laws in the US were different -- I am not sure how this works, but generally on albums from the 1960s, I don't see a copyright notice for the recorded sound itself -- which would be (P) in a circle rather than © -- but there is often a notice for the artwork, which is what this has to be. I'm not a lawyer nor a copyright expert, but I have read that prior to 1972, there actually wasn't legislation protecting the copyrights of sound recordings in the United States. That changed in 1972, and somehow it was amended retroactively. I realize what I'm saying sounds like nonsense, but I have read references to this in more than one place. Perhaps someone more well-versed in copyrights and legal stuff can clarify this.
Aside from that though, the entity that owned the copyright and the entity that retained the tapes don't necessarily have to be the same.
Someone on the Steve Hoffman Music Forum wrote a number of years ago that they saw a budget Banana Splits reissue CD on the MCA label, but only saw it once as if it was released and then quickly withdrawn. IIRC they said it was definitely different from the widely-circulated bootleg on the "Hollywood Library" label from the mid-1990s. Unfortunately, I can't confirm this.
Edited by Mark Y, June 30 2013 - 12:23 PM.