Well, unless I hear otherwise, I’ll assume that it means pick a skill. (It seems like it would be a bit overpowered if it indeed meant any (all) skill check(s) made for the duration.)
Yeah, given that the penalty can be increased with increased Mastery, I’d hesitate before allowing it to hit everything. As a house-rule, I might allow the witch to penalize every skill roll in exchange for lowering the duration to a single scene.