I have a few thoughts on this though. One would be the legibility. Of course I cannot judge legibility of writing systems I do not like, but it seems that nastaliq would be hardly readable on a lot of mobile devices and I wonder how difficult learning the ornate script is. I am talking about alphabetization here.
Next thing is: I am learning turkish and turkish is written in the roman alphabet. As far as I know, it was written in a arabic/persian script before which was then reformed to use the latin alphabet. As far as I can tell this is today really uncontroversial and using the latin alphabet is actually the more suitable alphabet for turkish and its rich vowel system that is really important for grammar and meaning. Again I cannot really say anything for Urdu, but knowing it is not arabic but afaik a language of the indo-european family I wonder if there are more reasons to use the lating alphabet than just availability of nataliq fonts and rendering engines.
As a side note I would add a few observations relating to the cultural/heritage aspects. In Germany, the "Fraktur" was used widely even at the beginning of the 20th century (see http://en.wikipedia.org/wiki/Fraktur ). Some authors, like Hermann Hesse refused that Antiqua fonts would be used for their writings until publishers convinced them that their works could just not be read by young folks. In a way, a lot of people argued against using non-gothic fonts, but in the end antiqua became quite standard. Nowadays we use the lating alphabet (and most people are not concious about that there ever was a switch).