Vintage Duo-Sonics usually sell for about twice as much as vintage Music Masters of equivalent year. Yes they're the same aside from the pickup and Mustang switches. Music Masters were even routed and shielded the same as the Duo-Sonics into the mid 70s. There are less Duos on eBay because there were less made.
If you're talking about the 90s Squier Music Masters vs the 90s Fender and Squier Duo-Sonic reissues or the newer Squier Classic Vibe Duo-Sonic the reason that the MMs sell for more is that they were made in Japan as part of the Squier Vista Series and are higher quality than the Duo-Sonic reissues. The Squier MMs are scarce though, there are way more Duo reissues kicking about.
