Their company has been having issues for quite some time, not with just the Disgaea RPG, the mobile game. Disgaea RPG definitely contributed, but may have been the tipping point, rather than the overall cause. I say this because no sane company would put everything into the development and success into one game after two decades of success. Something else had to have had contributed to the lack of funds to pay their employees.
I'm not sure if any of the recent controversy has been impacting their teams to cater to worldwide releases of console versions, rather than just Japan. I believe that Sony has influenced many game developers and publishers to basically make two versions of their games if they want to multi-platform. Not long ago Sony moved their Playstation headquarters to the U.S. and imposed a more conservative stance than Nintendo. However, this is just a theory that may have contributed to NIS having monetary issues.
In addition, I know that at least NIS America was also experiencing problems releasing titles, like with their TBD release date of RPG Maker on console. But, this is NISA, not NIS, and I'm not too sure how much revenue and capital is shared between the two.