You’re right about the big 5 publishers colluding to keep e-book prices high, and Apple was caught up in that I believe, as there was a lawsuit a few years ago about that. But Amazon encourages low prices on e-books.
In fact, they only give their best royalties to e-books that are priced between 2.99 and 9.99. Independent writers, like myself, therefore sell our e-books far lower than the big publishers do.
Barnes and Noble problem was simply it cost a lot of money to keep retail brick and mortar stores open and if they don’t have the book you want, it can take weeks to get in. If you go to Amazon, though, they only have to pay for warehouse space so their prices are about a third less on paperbacks alone. And they can get you any physical book in two days for free if you are a Prime customer.