I'm not sure if the fields will be affected, maybe someone with more knowledge will chime in on that. I have used the ones with holes in them on my first two genny's, much smaller than what you are going to be using,1"x1" ring mags with 3/16"bore, that is what I have flying right now on my 8 1/2' mill, if there is somekind of negative effect I haven't noticed it.
Eric
Those are some beefy magnets, 3"x1.5"x.75", you must be building quite a large genny.