I'm not sure what has been replaced, if anything, but Frank Zappa's credit is still there in season 1 (Paramount usually changes the credits when they strip out music), and the relatively few non-Zappa licensed music uses seem to be there, like "Vacation (All I Ever Wanted)" in the Vietnam episode. The theme song, of course, is intact (not a given with Paramount).
There may be some changes I didn't catch, but for now this seems like a surprisingly good set for CBS/Paramount: Decent packaging, lots of special features, original promos, even decent menus (every time you click on an episode title, you hear a different Duckman audio clip before being taken to the episode), and at least some music clearance has been done. I wouldn't expect this kind of thing as a rule from CBS, but for now it looks like they might have done right by this show. If it weren't for their annoying habit of replacing the closing logos, I could forget that this was a CBS/Paramount product, and I mean that as a compliment.
After watching the first disc, I can see that Paramount went to some trouble for music clearances.
This really is a show I never thought I would see again, and definitely not completely released within 6 months.
Turnong to the last volume, I am worried for one episode near the end of the run. I believe it was Duckman in a haunted house or something like that, and at the end, a certain 20th Century Fox owned, yellow skinned, donut loving character we all know and love makes a cameo appearance. Since the second and final box is due out in January, that issue has already been resolved one way or another (I suppose), so either the cameo will be there, or it's been cut entirely.