Hmmm, interesting observations.
With missing instruments, wires and fuel lines hanging loose, I wonder if the pedals were even connected? The cable for the lower pedals is clearly visible in the Smithsonian panorama but we don't know if the other end was connected to anything.
The only concrete evidence I can offer on the issue of brakes is that the aircraft I flew, a 1927 Travel Air with mechanical brakes and a 1929 Travel Air with hydraulic brakes, had the exact same pedal arrangement, and the top pedals were the brakes in both aircraft. Come to think of it, the four other Travel Airs I've flown that belonged to other people were set up like that too. But, of course, that's no proof Lockheed used the same arrangement.
That said, it seems like it would be very awkward to fly if the lower pedals were the brakes. They'd be in the way of your foot on the rudders above. (Not that the cockpit is a paragon of ergonomics in an event.) Heel brakes are generally a bit off to the side out of the way and you move you foot like when your using heel-toe changing gears in a sports car.
General information about the Wing42 Lockheed Vega.