Cultural appropriation is always a shaky topic, because it's one of those things that so many people have opinions about, and there still isn't a real consensus on it. Therefore, bearing in mind that this is my theory--and thus an opinion--here's what I think:
NINJAGO has the benefit of being based upon a facet of culture that is pretty heavily ingrained within society as a whole. The concept of ninjas has, by this point, transcended Japanese culture, becoming something that everyone is familiar with. Think of it like the knight in shining armor, or Santa Claus--everyone knows what a ninja is, what they're famous for, and how they basically look, act, etc. This does, of course, mean that there are many misconceptions about ninjas, and that they often seep into depictions of them in media. This isn't generally seen as cultural appropriation, however, because of how prevalent ninjas are (just think of how many things have been inspired by them--everything from NINJAGO to Power Rangers). Similarly, most people wouldn't bat an eyelash at a slightly altered version of Santa--we know what the inspiration is, and because the figure has become universal, we don't see it as offensive.
Of course, there's room for debate on this issue, but generally, I like to consider the general reaction of the culture in question when thinking about things like this. Has Japan expressed a great amount of offense over NINJAGO's use of their cultural heritage? If so, then it may be worth looking at. If not, I would hazard a guess that it's fine...
This is a solid point, but I would like to present a counter-example in the form of Avatar: The Last Airbender, a show heavily inspired by Eastern cultures which was created by two white, male Americans that clearly have very deep knowledge and respect for their inspiration.