Note:In this post,I am not going to consider Savarkar’s position. Having put that out of the way,let me put it out:In the classical darśanas of Hindu philosophy,not all of them accept an Īśvara,yes(a supreme God),but all of them were āstika,not nāstika(accepted the Veda as pramāṇa in some format or the other-at least accepting the śruti and allied traditions as śabda uttered by an āpta). And the allied traditions of sāṃkhya and yoga accept the realms of devas,with the sutrakara in the third pada of the Yogasutras saying ‘jñāne sūrye saṃyamāt’ and the various commentators describing the knowledge of the realms of the devas which is gained in the method referred to in this sutra. Vaiśeṣika/Nyaya too end up taking the praxis of yoga for soiterological purposes,so nothing more needs to be said here,and Vaiśeṣika too admits the importance of the Veda. Purva Mimāṃsā may not accept an Īśvara,but its atheism is more of the ‘ackschually,there are no separate devatas apart from the mantra and the ritual.The deity is the mantra’ sort of thinking. And as to the position of Īśvara in Śaṇkarādvaita,this article explains it very nicely. I need not talk about the various other Vedantic schools.
Most people who take up the ‘Hindu atheist’ label are basically cowards who are too ashamed to admit that all their traditions spoke of devatās(regardless of whether they were capable of giving all the goals sought by their traditions or not). Not a single one of them denied the existence of devatās.