Unfortunately yes. Each package needs to be retrieved, catalogued, recorded on your reservation, stored and later retrieved. My experience has been that they charge $6 for each package as they will arrive individually so these steps need to be repeated each time.
I’m not sure what happens if a package comes in 2 or more boxes that arrive together as mine always got separated in shipping. You might just be charged once but I honestly don’t know.
As a Canadian I used to order more shipped to Pop as some companies don’t ship to Canada or, charge a huge amount. (Once tried to order 2 t-shirts from Disney and they were going to charge $25 for shipping! No thank you!) I will say I’ve greatly reduced the amount I order and have shipped to the hotel since the $6 fee was added although when I realize all the steps they need to take it does make sense. For me, this fee has worked as I have less shipped so cause them less additional work.