Okay, we finally have some download numbers for NSMB 2 and Onitore.

NSMB2 - ~5% DL sales (Almost 40,000)
Oni Training - ~20% DL sales (Almost 20,000)

Overall for NSMB 2 = +800k (from the latest Media Create)
Overall for Onitore = 115k (from the latest Media Create)

http://jp.wsj.com/IT/node_496395

Note: It is not confirmed whenever this also includes download cards.

Translation from article (Google Translated):

According to Mr. Iwata, 3DS for this approach has been introduced since the beginning of the year already, we successfully called on it.

For example, recently launched in Japan in the United States over the net sales of the title "New Super Mario Bros. 2" is started with selling new release of the XL has accounted for 5% of total sales.

Mr. Iwata, then it's a promising sign for the team of Mr. Iwata and he pointed to the point of the title does not change the selling price over the net in stores.

Mr. Iwata said, "This first net sales, have shown positive response over time and".

Which accounts for about one-fifth of total sales turnover of well over the net of the "training 5 minute train the brain demon terribly" another title. Mr. Iwata, sees some thing can not because every day in the sense of a puzzle game, the reason for strong download sales of the same title. Mr. Iwata explained that users are, or not do not want to carry a game cartridge along with the terminal every day.

Famitsu includes the download cards sold at retail, not downloadable copies purchased directly with Nintendo. 
http://www.neogaf.com/forum/showpost.php?p=41127605&postcount=383

Not sure what to think...

That would mean that those download cards sold in stores are probably considered physical sales.

Edit: ^Alright.

Famitsu includes the download cards, which the sales are...

790,732 for NSMB 2

98,088 for Onitore

If we included the numbers straight from the eShop (that's if these are straight from the eShop), then we'll get...

+830k for NSMB 2

Around 120k for Onitore 

Using Famitsu numbers this is hard to track exactly how much the overall sales are. Could mean more copies sold or not.

Wait, I'm confused...

The 5% for Mario and the 20% for Onotori are for the in-store cards and NOT direct eShop numbers from Nintendo, right?

So sales will still be a bit higher once Nintendo releases DD sales (and it would be up to us to subtract the in-store card downloads to get a more detailed breakdown)?

Some places in Japan either have it lower or higher.

why wouldn't the cards be considered sold at retail, you buy the game card physically there for the full price and just download at home.

What I did get from the article was that Nintendo are very happy with the numbers and these show a positive response over time.

If there's no price difference between physical and retail, and you live right in the city (this is Japan after all), then I'd say the numbers aren't too surprising.  Personally, other than Club Nintendo giving us +50 coins for the digital eShop download, I have no desire to lose the physical copy and move to digital.  It means I can't sell it back if it turns out I don't like it, and I don't have a nice box to set by others in my collection.

NSMB2 (40k) ... OUCH!!! I expected something between 100k - 150k. Digital sales for Onitori, on the other hand, are good relative to overall sales.