Naruto's chakra restored to him at least 10 times over the naruto 699 and naruto 700 course of the war. As well as receiving healing from Sakura twice, on top of the fact that simply being a jinchuuriki grants him enhanced stamina and healing. You also remember the fact that Naruto is an Uzumaki and thus was born with enhanced longevity from the beginning. All while drawing natural energy from the planet to multiply these chakra boosts exponentially.
You can't play up someone with near limitless chakra wasting said chakra
as a weakness. It would be like me saying "Sasuke had his Sharingan on
through the whole war!! He wasn't 100% during the fight!" It's so
insignificant a burden it isn't worth mentioning.
Failing to use attacks that would guarantee you victory in a fight?
THAT's a hindrance. Allowing yourself to get tired when you have the
means to avoid that while inhibiting your foe at the same time? THAT's a
hindrance. Relying on a weapon that you haven't fully mastered while
your opponent is using a power he's had experience with since birth?
THAT's a hindrance.