There are 5 graphemes which we know as Nuqta consonants in Hindi (written in Devanagari) – क़, ख़, ग़, फ़ & ज़ [ qa, k͟ha, ġa, fa & za] which are used for writing mainly borrowed words. Out of these 5, फ़ fa & ज़ za are the most commonly used in published literature, while the rest are less common.
According to government of India’s Language Standardization Committee for Hindi – report of 1966 & 2010, all 5 [क़, ख़, ग़, फ़ & ज़ / qa, k͟ha, ġa, fa & za] are included in the modified varṇamālā of Hindi. The committee suggested that these graphemes should be used when & where required. In words where traditional spellings have replaced them with nearest allophonic variant (nativized), the nativized spelling should be retained e.g. किला kilā not क़िला qilā, दाग dāg not दाग़ dāġ, or कलम kalam not क़लम qalam. The committee also suggested that in words where it was important to show the distinction, the nuqta graphemes must be used e.g. ख़ुदा k͟hudā (God) vs खुदा khudā (dug) or फ़न fan (skill) vs फण phaṇ (snake’s hood).
On the other hand, the usage of these dotted consonants has always been controversial and a matter of debate, since several language scholars oppose their use in Hindi, as many speakers of Hindi simply pronounce them with their nearest allophonic variant क़ > क qa > ka, ख़ > ख k͟ha > kha, ग़ > ग ġa > ga, फ़ > फ fa > pha & ज़ > ज za > ja. But the acquisition of some of these consonants (e.g. फ़ fa, ज़ za) is on the rise even among non-urban Hindi speakers. Another interesting aspect is the development of free variation in urban Hindi between pha फ and fa फ़. I have observed in urban forms of Hindi, that it usually occurs word initially or at morphemic boundary as in फ़ल fal vs फल phal , सफ़ल safal vs सफल saphal, फ़ेंकू fenkū vs फेंकू phenkū.
I believe this is an influence of English rather than Persian because the distinction of Ph फ vs Fa फ़ is maintained in Pakistani Urdu, whereas in Delhi सफल saphal (the vegetable mart) became Safal सफ़ल. Or the common (mis) pronunciation of फिर phir as फ़िर fir.
As a whole, we can say that the usage of these nuqta consonants is on the rise in the published world. It is mainly due to following factors –
Increased access to education and acquisition of urban forms of speech (+proliferation of English words).
Process of standardization happening because of web based services such as Google Indic IME, MS Bhasha etc.
Dominance of progresstive writers over the last 6 decades in Hindi print media and literary world, who are not repugnant to the usage of nuqta bearing (foreign?) words in Hindi.
Ease of typing nuqta (dots) on devices because of Unicode encoding, compared to the times of typewriters and old printing presses.
To summarize, it can be said that the usage of क़, ख़, ग़, फ़ & ज़ [qa, k͟ha, ġa, fa & za] is still not standardized in Hindi, but there are some changes happening now. One can even see it on android devices and computers where Google Input tool auto suggests ग़लत ġalat as a top tier option with गलत galat below it.