I was wondering about the Wizard Pipe. Since it targets a card in my hand, can I use the Wizard Pipe if I have cards in my hand but my deck is dmpty?

You can only do an exchange if both sides of the exchange exist. In this case, the top card of your deck doesn't exist so no exchange can be made.

Sadly once your deck runs out, the Elrond/Vilya effect stops being useful, and Gandalf stops being able to pay for non-neutrals.

Start packing Will of the West if this happens more than rarely.