Re: What happened to the show's sets? Where they thrown out ?
I think, at this point, all of the existing sets from the various Trek incarnations have been destroyed and/or thrown away. A lot of Trek props, set pieces and costumes were auctioned off. Some are being used for the Star Trek Tour. And I'm sure there is still a big warehouse full of stuff on the Paramount lot. But the overall sets themselves are gone. TNG's sets had to be destroyed to make room for VOY. VOY's sets had to be destroyed in order to make room for ENT. And once ENT was over, the sets weren't carefully disassembled and put into storage. The show was cancelled - they figured they wouldn't need them again.
The Enterprise-E sets were taken apart and put into storage between films. I suspect, at this point, Paramount may have had them thrown away. We'll never see the TNG crew on that ship again, so why take up valuable space? I don't think J.J. Abrams needs them!