Well,  the bulk of nepalese population(including Khas,kham, kirats and newars )are not original vedic hindus.they took over hinduism from the displaced hindus(licchivis,mallas,rajputs and maithali priests)and saints from india in late 10. or 11. century.

so there has always been a big influence of animistic traditions and shamanism.but  hinduism is essentially a mixture of all these animistic traditions combined together.thus come the followers of mother goddess,shiva,  indra ,vishnu and all other gods together.The rishis and yogis later formed the philosophical basis of this ``sanatana dharma`` in which they accepted the existence of all these heavenly forces and still put forward  the existence of the one single timeless lord.