1st Gen if I got another DS

Would I be able to download the already purchased virtual Yellow / Blue onto it?

I believe the only way you'd be able to download an already purchased game from the eShop would be to do a system transfer to your new 3DS, which moves over all your settings and Nintendo ID information to your new console. The only problem with that is you can no longer use that account on your original 3DS. I'm also not sure if you lose access to your downloads once you do this as I've never tried it myself, but I'll let someone else answer that if they've done a system transfer.

I believe you would not be able to link up your account to multiple systems like Playstation or Xbox does. You will need to do a system transfer to that second 3DS and then download your games again, making the other 3DS open for another account. So you will not be able to have the same account on two 3DS systems therefore meaning that you cannot have your downloaded games on two systems either.

Yup. This was the bad thing that Nintendo perpetrates. They have that annoying one-lock system thing going on, unlike their competitors.

I hope this article helps.