That's what a host of sites are reporting after Twitter sleuth,
Superannuation, uncovered a resume from an environmental artist at Griptonite Games talking about work on a "Shinobi 3DS" title where he "created whole levels for 'Shinobi' on the Nintendo 3DS, including many props for use in a variety of environments".
Griptonite Games are also no stranger to handhelds, having worked on a number of big-name projects including Assassin's Creed: Blood Ties for PSP, Spider-Man: Shattered Dimensions for Nintendo DS and more recently for 3DS, Green Lantern: Rise of the Man Hunters. It would be sweet to see the classic ninja re-emerge from the shadows on Nintendo's new handheld. Hopefully we'll hear more at E3.