From all the times I've used Nippon-yasan, they never included invoces for the items I ordered. So I doubt customs will be able to do anything due to lack of invoice + marked down prices + package marked as gift. I have only ordered games from them though, so it's probably a good idea to hear from another GAFer who has imported consoles from them.
Also keep in mind that the New Nintendo 3DS is released on a Saturday, so depending on whether their local post office is open on Saturdays (edit: though I assume they are using
one of those that are open on Saturdays) or not, the package may be shipped on Monday instead (unless you request them to ship on Friday?). Add to the fact that Nippon-yasan is located in
Matsuyama in Shikoku (one of the four main Japanese islands). So even with EMS shipping the package first need to be shipped to Osaka (what the item tracking page usually shows), which takes anything from half a day to a whole day. Then it'll take another 2~4 days for the package to arrive in your country.