Grasshopper updated their company fact sheet a few days back, and it includes a notable change. Among the 'major clients' on the sheet, we now see that Nintendo is listed. Previously, Grasshopper's major clients were those who published Grasshopper's games. While Nintendo is distributing the physical version of Travis Strikes Again: No More Heroes, they are not actually handling publishing duties.
Whether this update points to something more going on between the two companies, or is simply tied to Travis Strikes Again, remains to be seen.