A dual MC setup gives you an extra brake circuit in case one fails (i.e., if the rear brake line bursts, you’ll still have front brakes, and vice versa). I’m too new to karting to know if this is a safety requirement by many series, but I know in the formula car world it’s almost a universal requirement on safety grounds.
A dual MC setup will also allow you a larger range of adjustment. With a single MC if your rear brake pistons are the same size and quantity as either front wheel, you’ll basically have the option of 66/33 F-R split to 100/0 F-R split. If you have two MC’s you can basically run anything from 100/0 to 0/100.