No,.. you would not help or hinder the naked short posistion by getting you share certs,..
When you ask for these the Brokerage firm gets them sent to the T/A (Transfer Agent) who changes the nameé on them from street name to your name. (street name is the brokerage firm,.. all firms do this for accounting purposes) after they are changed to your name they are sent back to the brokerage firm to be sent out to you.
Now on the flip side when you re deposited them they are sent from your brokerage firm to the T/A to get the name changed again from your name to street name,.. then they are sent back to the brokerage firm to be deposited into your account... in the mean time it has the very same numbers as when you had them in your account ot start.
I see no advantage or disadvantage to this procedure.