ok let me answer your question, no the game will never be hard to find
1) if the game is good, it will continue to sell copies that is just common knowledge. also if you are having a hard time finding a copy in a store like walmart, look at something like gamestop someone may have decided to sell their copy if they didn't like it or have 100 percent completed it and don't want to do it again. gamestop is normally good at keeping these games in stock also with newer copies.
2) the game will always be on the eshop, unless something happens that requires them to only sell it retail (see kingdom hearts 3D cave story 3D etc) now before you say i don't like buying digital let me say this, there is no difference between a digital copy or a physical one unless you are worried about your block space on your 3ds memory card or not getting your money back. both are working copies, both will play the same digital is sometimes easier to come by however due to stores never knowing if a game will stay in stock or when they will get more.
all in all no this game will not become hard to find, you should always be able to find a copy.
(small editors note - if you guys are not sure you will like a game, if you have a buddy that has a copy as them if you can watch them play and or play it yourself while you are hanging with them to see if it is for you. that way you save your wallet some pain in the long run, always remember do your homework before you buy anything.)