Yes it's LTD. The digital manual states this under All Software: "Lists the most-popular software to date."
Recent Releases states this in the manual: "Lists the most-popular software of the past two weeks."
The eShop automatically updates every two hours.
For reference, the game is currently #1 on the Recent Releases charts and #9 on the 3DS software only listing in the All Software charts. It'll have to outsell New Super Mario Bros. 2 before it appears in the All Software listings.
Read my original story on Fictionpress (Shinigami Twin): http://www.fictionpress.com/s/2996503/1/Shinigami-Twin
As well as my other one (Hell's Punishment): http://www.fictionpress.com/s/3085054/1/Hell-s-Punishment
Nintendo Network ID: kingofe3