Signs are mostly useful for people who are new to a place, if you need a significant amount of time to familiarize yourself then they are useless.
There are multiple ways to get to various lines' platforms. This is not signs pointing to each other, this is signs in different places pointing to the same destination.
I live in Tokyo and while I do not go through Shinjuku often as I mostly live and work on the east side, I have no issue using the signs to find the platforms and exits I am looking for.
If you pay attention to what the signs have written on them, they will take you where you are trying to go.