It's probably something like that.
The last two times Nikkei reported something about Nintendo, which Nintendo then denied, Nikkei was proven to be correct more or less in the long run.
Nikkei said Nintendo would be releasing a Nintendo 3DS XL, Nintendo denied this the next day, and then 5-6 weeks later unveiled the ... 3DS XL.
Nikkei said Nintendo would be making smartphone games. Nintendo denied this. About 8 months later, they announce that they're making smartphone games.
So I wouldn't be shocked if Nikkei's report of Nintendo using the Android OS in some fashion is true.