Mini Ninjas appears to be getting a sequel in some capacity, titled "Mini Ninjas: Hiro's Adventure." A trademark from Square Enix, along with domain registrations, mention the new title. Exactly what Hiro's Adventure could be, however, is still in the dark.
Siliconera noted the trademark registrations. Eidos was the original publisher of Mini Ninjas back in 2009, but it has since been folded into Square Enix. When Google Chrome had its coming out party for in-browser games, Square Enix mentioned that Mini Ninjas would be available on the service sometime in 2012. It seems that despite mixed reviews, Square still sees value in the brand.