Theory on Permanent CS Equips

I know that, but it weird that they would do something like this because it seems it would lower their sales.

Not really. They have events all the time. I got my permanent transparent hat about a year and a half ago, I think. Definitely long before all cash shop clothes had a permanent option. Do you think they were getting ready for the end of Maple back then?

They do their math. They figure a lot of people will now rush out to buy NX and full equip their pets. That's immediate money in Nexon's pocket.
For a little while they might see a decrease in the sales of the 90 day items, but the demand will pick up again as people make new accounts and new characters of classes that don't share cash shop storage. Many of those buying perma gear this week will not even be playing 3 or 6 or 9 months from now, so that's pure profit for Nexon.
All in all, I believe that if there's one thing they know how to do, it's milk their players for maximum profit.