Well, socrates, the site apparently is a bit confusing for people like you and me: if you pay by paypal or creditcard you don't have to pay the bank transfer fee. Too bad for them they scare off people like you and me before we get that far.....
They have a regular deal with altera to develop the development-and-educational boards. So I don't think they can offer to ship FedEx and then just throw them in the mail. Altera would find out and be unhappy with them about it. Also you can ask FedEx to pick up your DE0-nano if you give them your FedEx account number. That way they don't see that extra $50-$70.
So the question remains: Why don't they offer simple "mail" service?
They are in Taiwan. Possibly their mail service is just as expensive as in the US. Anything I buy off Ebay in the US has enormous shipping costs. If it is even worse in Taiwan, then it might be that the extra reliability for just a few dollars extra is worth it.
On the other hand, they might have had bad experience with normal mail of clients claiming not to have received their goods and then they have to resend at their cost.....