It also seems that Nintendo, in their classic approach to online infrastructure, has decided to make these games complicated to get to and without any clear notification on the front store page. This guide explains how to do it:
First you need to go to the E Shop and then head to the "Settings / Other" option
Then you scroll to the "Your Downloads" Option and hit that
Once done, you'll see a list of all the NES games you can download by hitting the "Redownload" option.
So it's as simple as going through tons of menus that are not advertised anywhere else in the e shop and "Redownloading" these games, bravo Nintendo.
Menu navigation aside, I really think that Nintendo Europe has handled this worst of all, the games are later than the rest of the world, we've had to rely on America to get instructions on how to download these games and we can't even check yet if we qualify for these games. America and Japan have had dedicated sites where you can check if your 3DS is part of the ambassador program and look up help and info. Europe has had nothing of the sort, no communication from NOE, nothing to help anyone out who doesn't know the situation. I'm even starting to doubt that we'll see these free games tomorrow.