I currently have two 3DS and when I linked the second one in eshop it shows I don't have any downloads. Surely I should have access to all my stuff bought under my eshop account.
Am I missing something or do the games only work on the one 3DS that you bought the games on?
Downloaded games are only playable on the system that they were downloaded onto. What you linked your two eShops two was not one eShop account; it was your Club Nintendo account. That only gets you Coins for your games.
Wow, that is disappointing. Even Sony and Microsoft will let you play your content on more than one device. They don't require you to buy it for each and every device. Nintendo's online system has a ways to go.
Thanks for the answers.