The OP raised the following issues here:
why no Hindu deites are actively worshipped in Ramakrishna Mission centers?
Is this an old practice or a newer one (post-Vivekananda) in order to show themselves as separate from Hinduism?
Further, in comment section, the OP confirmed that the actual question is
Why the authority of RK mutt not ...
The question is
Is there any scriptural ( Vedic or Puranic ) reference for all matter
coming from Akasha being acted upon by Prana?
Let us go in reverse order, ie., from Puranas, which were composed at a subsequent date compared to the Veda, to the Veda. This method is adopted because the Rig Vedic vocabolary, being cryptic, cannot be understood ...
"Prana," this word being the Sanskrit term meaning "Absolute Energy."
Science of Breath, by Yogi Ramacharaka, William Atkinson, 
What is Prana? Prana is the center of everything.
"Prana is Fire; Prana is the Sun; the Cloud; the Wind; Prana is the Killer of Demons; Prana is the Earth. It is what is and is not, immortal. Prana is the ...
Here is one reference from Śrīmad-Bhāgavatam (Bhāgavata Purāṇa) 5.25 - 5.29:
tāmasād api bhūtāder vikurvāṇād abhūn nabhaḥ
tasya mātrā guṇaḥ śabdo liṅgaṁ yad draṣṭṛ-dṛśyayoḥ ||25||
From the darkness of false ego, the first of the five elements, namely the sky, is generated. Its subtle form is the quality of sound, exactly as the seer is in ...
Is there any scriptural ( Vedic or Puranic ) reference for all matter coming from Akasha and Prana?
Yes, the Taittiriya Upanishad says all elements come from ether:
tasmAdvA etasmAdAtmana AkAshassambhUtah | AkAshAdvAyUh | VAyuragnih | AgnerApah | adbhyah prithvi | prithivyA oshadhayah | oshadhIbhyo'nnam | annAt purushah
From that Brahman sprang ...