All the logo has to do is feel and look good at first glance for outsider. Simple as that. You will not be able to provide lengthy explanations and diagrams with it unfortunatelly. It just is what it is to a fresh newbie as he first interprets it. Cube is a cube, it's wishful thinking to suppose that people will pick the letters from it, no way. Tomoe is some kind of whirl, etc. You have to look it from outsiders' point of view.
You are right that the first glance works like u said.
The explanations and diagrams are for the later times, when the outsider has decided to be interested in NEM. That N, E, M letters to hexagon change can be explained very easily, with one picture. The picture can lead to wiki page "history of NEM" where is explained more
