If the seller does not perform a system transfer before he formats it, then his eshop history will still be attached to that 3DS.
I actually had to learn this the hard way when I got my 3DS XL.
To make it simple, I had a black launch 3DS. Upgraded to Purple 3DS when it came out. THAT system transfer went smoothly.
When I went to transfer from Purple to my recently purchased Red XL, things went bad. My mobile hotspot went down mid transfer, which errored out my transfer. It wouldn't be a big deal, except Gamestop was about to close and I had already been there an hour. I could not start the process over again, and had traded in my old system for the new one. I went home with the intent to call Nintendo Cust Support and see if there was anyway to get my Ambassador status back.
The next day a Ninty rep told me that this was not an uncommon issue, but as long as the transfer didn't take, my account would still be on my old purple 3DS. I went back to Gamestop. Luckily my old 3DS was still there, but it had been formatted of course. I initiated system transfer, and made sure my hotspot did not go into standby this time. It worked.
Keep in mind I did lose all my streetpass data and Find Mii hats and saved games, etc.
But to clarify the situation, he will have to transfer to another system, otherwise you can redownload all his eshop purchases for free.