Efficiency and heating is an issue of how much you try to extract from a given size machine and little to do with the size and number of magnets.
For a given set of discs and a given speed you can alter the number of magnets over a fair range for similar results as long as the volume of magnet is similar.
I agree with RP that you will be worse off with too many small magnets. You will have more leakage flux and you will also loose out with small magnets because the flux in the surface region is lower than in the bulk of the magnet and with small magnets a lot of the material is in this surface region.
The only case where you may benefit is if you are forced to use transformers, where the higher frequency will make life easier.
The 2 x 1 x 1/2" magnets tend to be far more cost effective compared with odd shaped things and you will do better to stick with them. Your tiny magnets will probably be thin as well as small. Thin magnets are not cost effective with air gap designs.
Flux