Well, it makes sense if some songs are exclusive, but it's not farfetched to think some songs might be on both versions but playing on different stages.
The Gerudo Valley song plays on the Gerudo Valley stage on the 3DS version, but could instead play on Skyloft or another Zelda stage on the Wii U version, since the Gerudo Valley stage is exclusive to the 3DS version. This assuming that the song is featured on both versions, of course.
Personally, I'd like if both versions shared the same soundtrack, but had the songs distributed differently due to different stages. Any stages on both versions, such as Battlefield, would obviously share the same music sets.
Though the 3DS can actually handle many songs on the game card, given that those have 8 GB like Wii dual layered discs such as Brawl's, I'd understand if it hadn't as many songs as the Wii U version.