Occasionally I've clipped just a small part of a wing and then you cannot be sure that she's clipped when you look later. To an extent the type of cut depends on how much the girl wriggles. I usually cut diagonally across both wings now and that seems to work. I've never had a problem with balling after cutting. Fast-moving queens are more likely to be chased than a slow moving one but that's all I've seen.
For paint I use the posca pens and they seem to work fine. I don't wait for it to dry before putting the queen back. They can also be used to mark a frame instead of trying to find a drawing pin in a hurry.