In general, I'm enjoying how the Hand fits into things this season more than the first.
They could have done more to sew them into the bigger plot (though admittedly I'm still not done with the season and they seem to have a larger role in things than has been revealed) and had more fleshed out members or go a little further into the mythology/philosophy to give the organization more weight to what they are rather than being mainly a mysterious shadow organization with disposable ninjas that show up to fight every so often.
Sure, there feels like a sort of disconnect as soon as these traditional ninjas show up fighting with ninja weapons and dealing with some supernatural shit, but this is also a world where the lead character can hear a heart beat from across a noisy room and he can "see" better than people can with their eyes.
Some of the writing could improve that part of the show, but in general, I think it's also a matter of how it is all portrayed. The idea that there are mysterious ninjas tied to the Yakuza that really operate in the shadows and tighten their grip (no pun intended) on NY's criminal underworld is cool to me. In the MCU, they might have the most potential as an organization since HYDRA since they are both hard to unveil and therefore hard to beat. It creates a looming threat, but yeah, "Oh those pesky ninjas are back again" is kind of jarring in this universe when they stick out like a sore thumb. Force them underground so they have to be more low key and they are aces in my book.