This is a nosy question
What time did you start looking for these releases in stores? Most of them were pretty early on in the G4 line so if you missed the start of the line, that may be why you did not see them
As to why they go for higher - supply and demand. It always happens with collectible toys and items. When something is no longer available retail, it no longer has a RRP and therefore sellers can charge what they wish and buyers will pay what they have to. You have a combination of people late to the party or who missed them on shelves who are willing to pay extra to complete a collection/set and those who panic a little that prices are just going to get higher and better grab them when you can.
All of these ponies dont go super high. Check out a lot of ended auctions rather than BINs and you will find more affordable and more accurate, in my opinion
, prices. Its really only the ponies between the Lily Blossom/Cheerilee and Trixie/Lyra waves [excluding them] which go high - mainly because we have seen them no other way as yet so getting them this way is the only way to own them. Same reason the international exclusives are pricey - no other readily available release.
Like G3, I am sure one day in the future forums like this and ebay and garage sales and thrift shops are going to be flooded with a lot of these guys, and their prices will consequently drop. We were paying these percentage increases on ponies during the early years of G3 for the same reason and now the self same ponies hardly hold retail.