Yes, but it's not ApplePay specific, it's merchant specific. If a merchant requires signature for a physical card payment then it's not going to change because you pay with a virtual card.
They could waive signature if they wanted, but a lot of places only did the minimum required so they could say that they "support Apple Pay". Hell, I'm not sure many places are really all that excited about the whole thing in the first place considering how much some seemingly hate accepting cards in general.