Well look at this way, if a Shedinja was hacked to have Counter and it was hit with a super effective physical move whilst holding a Focus Sash, it wouldn't lose any HP because it only has 1 HP to begin with. Because the physical attack dealt 0 damage and because Counter counters all physical moves for twice the damage done to the user, Counter would become a physical move with 1 Base Power, even though double 0 is... well... 0. This is because the physical attack used to deal 0 damage is still affected by Counter and because Counter can't really deal 0 damage without failing.