(For a trivial example, is اس the word /ɪs/ "this" or /ʊs/ "that"? In Devanagari, they're clearly different, इस vs उस. Urdu script can distinguish them, by adding a diacritic to the ا, but it's usually omitted, leaving the reader to infer the intended word from context. For a native speaker, that's not usually a problem, but for a learner it can be an added challenge.)
On the other hand, I suspect the Urdu script might be faster for an experienced writer to use, as there's a beautiful simplicity and smoothness to its cursive forms, compared to the relatively complex shapes of many Devanagari letters.
Not in my experience and certainly not as a student. I'm not an expert but at my school اس for something that sounds exactly as /ɪs/ would be considered completely invalid. Only اِس would be considered correct. Actually, I think اِز (more like iz) might be more correct phonetically.
Another issue is the allophony of the schwas surrounding ह (/h/) in words like कहना which is actually pronounced [kɛɦɛnaː] and not [kəɦ(ə)naː]. (note that this is also an instance of the schwa deletion)