The smaller the bore of the master cylinder the higher the pressure you can generate and this pressure is duplicated at the caliper piston. The larger the bore the less pressure but more volume. A master cylinder gives a leverage effect which is equivalent to the ratio of the area of the caliper piston divided by the area of the master cylinder piston or about 7.3 for a standard setup (38mm piston and 14mm MC). This becomes about 5.8 for a 5/8" MC with a 38mm caliper piston
With twin discs you need to be able to move more brake fluid (two caliper pistons), hence a larger bore, but you have double the braking area which more than compensates for reduced leverage
As with most things it is a compromise. If you plan to use twin discs I would, given the choice, go for a 5/8'" master cylinder (like the CB900/CB750F2/CBX and most modern master cylinders). If I had a std single disc setup I would stay with the smaller master cylinder (14mm bore). I have used a small master cylinder with twin discs, but would not recommend it unless you go to all braided brake lines.
I have also used a CB900 MC with a single disc setup and although theoretically it should be worse, there was not a lot of difference.
Hope this is of some help
Clyde