Yes, they are missing! What I believe is that it is Herbert's work!
Posters have been placed in the places were they used to be! Look at them!
I also remember that during 2010, Yarr, Keeper of Boiler Room, Keeper of Stage and other puffles of Aunt Arctic were missing, they were trapped inside the Mine along with Rory and other workers. This created Puffle Rescue.
What do you think?
It has been discovered by the EPF that the puffles were stolen by Herbert, and they are used to dig coins for him. You can re-capture these puffles by playing Puffle Chase. Also, more penguins are losing their puffles as more and more posters have been added across the island.