Why not make them with the weedguard hole and just leave it empty? That way if you have some left over; you could always put the guard in and use them as jigs.
Well, on some of the heads the hook shank may be exposed down in the bottom of the hole, so water's going to get in there and potentially cause rusting inside the lead. Otherwise, I doubt it would make any difference. I have a customer who orders heads from me, that he uses to make bladed jigs, and he asks that the hole be included, because he also uses the heads for other jig types. I've told him that I can make some both ways for him, but he insists on having the hole.
Of course you can fill it with epoxy or some other sealer, or not, which would just be your preference to do.
If you're losing a good many jigs anyway, I guess it has no bearing as far as the possibility of the hook rusting.