Namo Namah.
>>It's kind of confusing
that some ISKCON temples are now worshipping Him, even in Mayapur.
The below passage from Hari-bhakti-vilasa on verse 187 from 14th vilasa could be the reason why many ISKCON devotees feel obliged to perform Siva-ratri worship. It is from the dig-darshini commentary by Srila Sanatana Gosvami on the above mentioned verse that goes as follows:
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Translation: "I (Sanatana Gosvami) worship both the Lords (Lord Hari and Lord Hara), who have great love for each other and hence, worship each other in order to develop "bhakti" for each other. Well, what could be the purpose for Vaishnavas to perform Siva-ratri vrata? In answer to that the author writes --for the sake of developing attachment to Lord Krsna. By giving up Siva-ratri-vrata there won't be any result of worshiping Lord Krsna as there will be absence of attachment to Him. Therefore, Vaishnavas must perform this "vrata". By the use of the word "api" it was implied that even Vaishnavas ( worshipers of Lord Vishnu) must perform this vrata, what to speak of Shaivas (worshipers of Lord Shiva), Shaktas ( worshipers of Goddess Durga ), Sauras ( worshipers of the Sun-God ) and so on."
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However, the below verses from Bharadvaja-samhita of Narada-pancharatra could be the reason why Srila Prabhupada never introduced worship of Lord Shiva or Lord Ganesa within ISKCON though Hari-bhakti-vilasa recommends worship of Lord Shiva and Bhakti-rasamrta-sindhu (1.2.118-120) recommends worship of Lord Ganesa respectively.
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Translation: to begin worship of the Lord (deity) by not first worshiping Lord Ganesa or worshipping the Lord (deity) in the presence of a "kapAlika" or a non-devotee is an offense in deity worship. [ An exceprt from the commentaries of Srila Jiva Gosvami, Vishvanatha Cakravarti on BRS (1.2.118-120)]
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Following is --Bharadvaja-samhita of Narada-pancharatra, Parishista, first chapter, verses 89, 90 and 91:
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nānā-kāma-hata-jñānā nānā-daivata-yājinaḥ
narā bhagavad-aikāntye na sthāsyanti kalau yuge (89)
Translation (based on an available commentary written by some Sri-Vaishnava scholar):
In the age of Kali, people in general will have lost their intelligence due to having various material desires. Thus, they will be worshiping various demigods to fulfill their desires. Hence, such people won't be attracted to the exclusive surrender to the Supreme Lord Vishnu.
paraṁ bhāgavataṁ vartma dṛṣṭāpi kali-mohitāḥ
prabhavanti na vidvāṁsas tyaktuṁ pūrvāndha-vartmanīm (90)
Translation (based on an available commentary written by some Sri-Vaishnava scholar):
Even if some of them who may be intelligent, and thus do come to know about the topmost path of Vaishnavas (Bhagavata vartma), they won't be able to give up the path of demigod worship due to being bewildered by the age of Kali in the form of strong bad impressions received from their forefathers who themselves lacked vision in this regard.
bhaviṣyanti kalau kecit kvacid aikāntino hareḥ
mohayiṣyanti ca pare kutarkais tān ku-dṛṣṭayaḥ (91)
Translation (based on an available commentary written by some Sri-Vaishnava scholar):
In Kali yuga, somewhere (not everywhere) they will be some (not all) devotees of Lord Hari who will be following the path of exclusive surrender to the Lord, however, there will be others who will have gained perverse knowledge from the scriptures that are mainly in rajo-guna and tamo-guna and such people will try to bewilder the "aikantika" vaishnavas by giving logics that are contrary to the conclusion of various Shastra-pramanas.
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In summary, regarding Shiva-ratri vrata or Ganesa worship, though recommended by Gaudiya scriptures, the "adhikara" or eligibility of performers should also be considered, for without reconciling scriptural injunctions based on time-place-circumstances can lead us to destruction as Lord Brhaspati famously said:
kevalaṁ śāstram āśritya na kartavyo vinirṇayaḥ
yukti-hīna-vicāre tu dharma-hāniḥ prajāyate
das,
Jaya Nityananda Dasa
("Nandagrama" Varnasrama Community Project)