Can replacing the bearings on a hub untrue a wheel?
No you can't affect true.

The hard part of doing cone and cup loose bearings is setting the cones just right - not loose - not tight. Usually takes a couple of tries.

There are a few things you (or the guy before you, or the factory) can get wrong.


wrong number of bearings
different number each side
wrong size


There seem to be some people/bike mechanics who believe fewer bearings =  less friction, and the deliberately leave one or two balls out. Personally I think it is total voodoo b.s. , but surprisingly common in these parts. 

I put the wheel over a shallow tin/box when I open up the bearings to catch them as they come out so I know how many there were, and what condition (pitting)

I recommend replacing ALL the balls any time you clean them, as they are just so cheap. When you pass a bearing shop get a bagful of 1/4" (rear) and 3/16" (front) balls.

Balls fail first, then the cone, and rarely the cups.