Most likely the encoders come with a 6mm D-shaft. The flat is 4.5mm so this is the standard shaft, unless you go for a splined, a.k.a T18 serrated shaft. There are also 4mm and 6mm plain shafts, and 1/4" (6.35mm). Anywho, enough with the shaft sizes, it is a 6mm D-shaft if you got the recommended part.
The nut that you normally want covered is either a M7 or M9 so you want a knob with a base diameter 12-13mm minimum. Of course, you should go for the aesthetically correct choice and join the Albs "Waldorf" knob bulk order that was just announced :)
It is not easy to find "plain Jane" knobs without an indicator line for encoders.