Perhaps someone might be able to add updated stats from the National Mission for Manuscripts efforts?  Their survey page (http://www.namami.org/nationalsurvey.htm) says:

The Survey So Far

The Mission began the National Survey in 2004- 05 as a Pilot Project in 3 states—Orissa,


Bihar and Uttar Pradesh . A total of 53 districts were covered— 30 in Orissa, 13 in Uttar

Pradesh and 10 in Bihar. In the Pilot Project itself, the Mission unearthed 6, 50, 000

manuscripts and about 35,000 repositories.


Drawing upon the experience of the Pilot project, the next round of Survey in 2005-2006


was held in Delhi, Manipur, Karnataka and Assam . In Delhi, about 85,000 manuscripts

were found. The Survey in Manipur was extremely successful despite several pockets being

inaccessible and about 10,000 manuscripts were located. Likewise, in Assam, about 42,000

manuscripts were discovered. Around 1,50,000 manuscripts were found in Karnataka. In

Gujarat, the survey was initiated by the coordination of the Lalbhai Dalapatbhai Institute of

Indology, Ahmedabad.


In 2006-07, the National Survey took place in Himachal Pradesh, Haryana and Tamil Nadu.

The Manuscript Resource Centre in Himachal Pradesh, Himachal Academy of Arts, Languages


and Culture acted as the coordinating body in the State. The National Survey was successful

in locating approximately 20, 000 manuscripts across the State, with local scripts like

Takri coming to the focus. The Survey also saw the school students getting involved in

the awareness campaigns to promote the documentation and conservation of manuscripts.

The Manuscript Resource Centre, Dept. of Sanskrit, Pali and Prakrit, Kurukshetra University

was also active in organizing the Survey in the State of Haryana. The Survey has been

successful in locating approximately 500 manuscripts. In Rajasthan, the Survey was initiated

by the coordination of the Rajasthan State Archives. Out of total 33 Districts 19 Districts

are already surveyed and an amount of 7, 50,001 Manuscripts are identified.


1
In 2007-08, the Mission conducted National Survey of Manuscripts in all 18 Districts of

Chhattisgarh and in all 16 Districts of Arunachal Pradesh. In Chhattishgarh, the Survey was
 
conducted by the coordination of the Directorates of Archives and Museums, Chhattisgarh and

in Arunachal Pradesh, it was conducted by the Coordination of Dept. of Cultural Affairs,

Directorate of Research, (Culture, History, Archeology, Museum, Archives & Philosophy),

Itanagar.


1
In the financial year 2007-08 survey was initiated in the State of Madhya Pradesh by the
 
coordination of the Directorates of Archives and Museums, Bhopal; in Goa by the Directorate

of Archives & Archeology, (Govt. of Goa), Panaji and in the State of Jammu & Kashmir by
  the Central Institute of Buddhist Studies, Leh.


1
In April 2012, the Mission has completed the Survey work (which was initiated in the year 2007)

in all 13 Districts of Uttarakhand by the coordination of the Uttaranchal Sanskrit Academy,

Haridwar and started processing for the survey of Sikkim and Mizoram



On Sun, Jan 20, 2013 at 9:20 AM, Dominik Wujastyk <wujastyk@gmail.com> wrote:
As far as I know, nobody has counted how many Indian MSS have been catalogued.  However, it should be possible to do some kind of back-of-an-envelope calculation for this, as follows.

There's a publication by Madras University called the New Catalogus Catalogorum (NCC)Its current editor is the energetic Professor Siniruddha Dash <dash_sans@yahoo.co.uk>.  The NCC is a digest of all published MS catalogues.  Well, not all, but most.  At least, up to the late 70s, and some later ones.  So, in NCC you can look up an author or the title of a Sanskrit or Prakrit work, and you'll get a list of the known MSS of that work, culled from the published manuscript catalogues. 

The NCC isn't finished.  Only nineteen volumes have been published, bringing it up to the end of ma (म), 37th letter of the alphabet.  There are 8 more letters of the alphabet to go, so NCC is about 37/45x100=82% done.   Each volume is about 350 pages.  Each page has about 50 MSS mentioned (this is *very* rough! - per-page counts vary wildly).  So each volume mentions 17,500 catalogued MSS, and there are 19 vols, so that comes out at 332,500 MSS mentioned so far.  And that's 82%.  So the total would be 405,487.  Say half a million.

There are *lots* of rough edges to this figure.  It's very, very crude.  But it does give one at least something to hold on to.  Half a million catalogued manuscripts out of a minimum total of 7,000,000.  That's 7%. 

But if the Koba people have put their MSS into a database - which they're doing at quite a rate, that could quite soon add 250,000 MSS to the total catalogued.  And there are other projects like that (though none so big, or well-funded).   So the total catalogued could be higher.  Say it's double.  A million.  That's 14% of the seven-million figure.  But the seven-million figure is probably very conservative.  So we're still hovering in the 5%-15% range, I'd say.

Improvements to the above argument and result are welcomed!

Best,
Dominik Wujastyk



--
James Hartzell, PhD
Center for Mind/Brain Sciences (CIMeC)
The University of Trento, Italy