Yes you can. It doesn't make a lot of difference if you only put magnets on one disc. It is virtually the same except that you can regard it as having magnets of half the length. 1" magnets on one rotor with a plain disc would be similar to 1/2" magnets on 2 discs.
The field is less uniform with the magnets on a single disc so the result will be slightly worse but this may be compensated for to some extent by the better utilisation of the material in the thicker magnet.
The set up is far superior to a single rotor with no return path.
If you use the same magnets for a dual rotor and a single rotor with return disc, then doubling the number of poles will likely give you more output, but at the cost of larger rotor discs and a thinner stator.
Flux