Ninja has as goal to be simple and fast, but not necessarily convenient for humans to write. It's in the second paragraph of their home page.
While ninja is great for many uses i would not recommend to use it for hand written rules. In fact any simple dependency-resolver like make or ninja will be lacking a lot of language context about includes and other transitive dependencies so you always want some higher level abstraction closer to the language as your porcelain.
ninja specifically handles includes automatically.
Anyway, not having any other automagical behavior and hidden rules and the fact that it can do incremental and correct job re-runs even when the rules change is exactly why I like to use ninja.
I especially love it in projects involving many different compilers/architectures/sdks at once (like when doing low level embedded programming), where things like meson or autotools or arcane Makefile hacks become harder to stomach.
Take meson. It's at the same level of cmake, but what handles the C include dependencies for it is ninja. cmake also has ninja backend. Not sure how it works exactly, because I don't use cmake, but I assume it will be ninja handling include deps too in that case.
Yes, ninja basically handles it for you, compared to what you have to go through when using Makefiles, to have autogenerated dependencies.
While ninja is great for many uses i would not recommend to use it for hand written rules. In fact any simple dependency-resolver like make or ninja will be lacking a lot of language context about includes and other transitive dependencies so you always want some higher level abstraction closer to the language as your porcelain.