"Is all phenomena limited to space, time and causality?"
"Is the idea of the holy and spirituality nothing more than pious nonsense?"
For us humans, the universe has dualistic reality. There's an experiential world about which science can say very little, except with regard to its correlation with observable phenomena. For example, to conduct an experiment about 'pain', science begins with the firm knowledge, based on common experience, that such a thing exists. Yet what can it tell us about pain? It can describe only observable phenomana that correlate with the experience. Should one then conclude that only the observable phenomena are real, and that the original experience that prompted the experiment never happened? There's an illogical incongruity there that resembles an Escher print. Consciousness, and all it's abstract phenomena are real, including holiness and spirituality, but they are not 'real' as defined by science. This is the dual nature of our reality.
Disclaimer: the above is not a dogmatic assertion fact
O day and night, but this is wondrous strange!
And therefore as a stranger give it welcome.
There are more things in heaven and earth, Horatio,
Than are dreamt of in your philosophy.
...Not only is there science, there is also poetry...