Wasn't there over 25 thousand star destroyers, during the DE.
Other sources put it far higher.
Thats like 1 ship for every 4 ninja lmao, they could carry around 10 thousand crew members, yeah 99% of the ninja are screwed, they can tag Jedi, Ninja's should be easier. Not to mention Turbo Blasters which are around 3 gigatons per shot, not to mention, the amount of Dark matter that they mine etc, and vast amounts of other weapons of mass destruction. Biological etc.
Naruto verse doesn't stand a chance, they would be overwhelmed. Not to mention the range of Naruto/etc's bjuu bombs/attacks compared to the GE, The Death Star would destroy them from out of range.