Unfortunately, as you have noted, without the original system to transfer to, you are likely without hope. 3DS titles are tied to console, not to any ID (Nintendo Network ID or otherwise), so without the console, you can't do a whole bunch. If you had the console, you'd be able to do things differently, but as it stands, there isn't much you can do.
There are stories online where people say you can contact Nintendo to get your stuff back, but since Nintendo themselves seem pretty hush on the matter (their website states that you can only do things through transfer), I don't know how lucky you will be. Club Nintendo keeps a sort of record, in a way, so they might be able to help that way.
I would also keep in mind that stores usually wipe any used consoles they receive, so even if you can get to the store, it is not necessarily true that you can even get your stuff back, even if they have your particular console still, as doing a format wipe of the SD card and the system means that your information will also be gone. This prevents the next owner from being able to essentially get free games by downloading what you had already purchased.
According to Nintendo Support:
A Nintendo Network ID is required to download game demos and other
free software.
Once deleted, Nintendo eShop purchases can be redownloaded at no cost.
Downloaded items appear as a gift on the HOME Menu. Once they have
fully downloaded, you can tap them to access the software.
What to Do:
- From the HOME Menu, select the Nintendo eShop icon and tap "Open."
- Scroll left and select "Settings / Other."
- Scroll down and select "Redownloadable Software."
- Select "Redownload" next to the software you wish to redownload.
- Select "Download."
- Select "Download Later" or "Download Now." Items downloaded now will begin immediately. Items downloaded later will begin when the
system enters sleep mode.
TL;DR: You need the original Nintendo Network ID to redownload the previously downloaded softwares after a console format.
You can transfer data between two consoles before a console format, but that will transfer the Nintendo Network ID account, too. You cannot transfer data on a console with another Nintendo Network account.
You cannot perform a system transfer if the target system has a Nintendo Network ID linked. You must format the target system to remove the Nintendo Network ID link prior to transferring content.
Best Answer
The digital purchases on the eshop are tied to the account. If you change the account you will lose access to the games.
As per Nintendo Support: