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Either in their massive collars, or their boots. now that I look at it, those boots look like platform boots. Maybe the bottom comes off and they keep 'em in there.
Maybe they have them in pockets that Sugimore just didn't draw? Or in hands like in the sprites? But I'm gonna agree with Epsekop and guess that the balls are where the balls usually are in their turtlenecks. Unless they can use magic...? O_o'
Galactic Grunt: You'll never interfere with Cyrus' plans! Now stay here while I take off my boots! *Begins unlacing 28 eyelet boots to get some slack so he can bend his knees*
Hero: *Runs past grunt*
Maybe they have huge fanny packs under their shirts stuffed with their horrible pokemon?
In their underwear? just kidding! As for the hair, that would be a problem when you forget they are there " Where is that Pokemon!?!?!" But that would explain cacnea attacking james' head (even though hes not a galactic grunt)