Atheism is not a religion but the single belief that there is no all-powerful sentient being organising the human world, which is a staple of Western religions. The corollary being that anybody believing in God is delusional and/or manipulative. This usually stems from the realization that religious leaders are abusing their followers, using cognitive dissonance to force people to do things that run counter to their most basic interests while serving parasitic power structures.

Unfortunately atheism has the side effect of weakening the social constructs that organized religion brings. Not being a religion itself, it does not prescribe any replacement rituals.

The Japanese stance you describe would better be described as agnosticism, the belief that God's existence doesn't matter. This allows to mix and match existing rituals and beliefs into a coherent whole and puts the individual back into the driving position. It's a very sane way of handling fragmentation of belief and what I believe more people should be doing.