In a most peculiar bit of news, Nintendo Everything (via SEGAbits) is reporting that Project X Zone (the original, not its recently-released sequel) has been pulled from the Nintendo eShop in North America and Europe without warning. I just checked this myself, and aside from a couple of trailers for the game, nothing remains -- not even the free demo, which Nintendo still advertises as being available on their website entry for the game.
More alarming would be that the re-download button for those who had downloaded it previously has been replaced with the message "This software is currently unavailable," though it appears that this can be circumvented by going to your “Redownloadable Software” list on the Nintendo eShop.
SEGAbits speculates that the reason it has been pulled could be a matter of rights issues, which they note is "why many song tracks were removed when localized in the west." A more bizarre bit of reasoning suggests that perhaps there is a desire to instead shift focus to the newly-released sequel instead.
In the meantime, you can still try to track down a physical copy of the game if you've got a desire to play more of the saga with Mega Man X, Zero, Tron, and her Servbots in tow.
I've reached out to Bandai Namco Entertainment America about the matter, and will let you know if I hear anything back.
Update: Well, I've heard back, and this is what they had to say:
"Project X Zone is no longer available for purchase through the Nintendo 3DS eShop as of this past weekend. Players who have purchased Project X Zone digitally through the eShop may continue to re-download the game to their account and physical copies of Project X Zone continue to be available for purchase at both retail and online stores. Project X Zone 2 is still available for purchase digitally through the eShop as well as through retail and online stores."
Doesn't really answer much as to the why, but at least it confirms that this is not a fluke, and the only way to enjoy this game now if you haven't downloaded it before is to purchase it physically at retail -- arguably the biggest argument against going digital with games.