One of the major disadvantages of using Shahmukhi to write Punjabi, as critics point out, is that unlike Gurumukhi, it's not phonetic. In addition to that short vowel sounds aren't usually represented and there is no letter for the consonant [ɳ]. As a result ھن may be pronounced [hʊn] (now) or [hən] (are). All this can be pretty confusing for a student. What is rarely mentioned, however, is that there is a flip side to the story too.
Let's begin with what critics gripe about the most: an un-phonetic script. While it's true that there are three letters for S (س،ص،ث), four for Z (ز،ذ،ظ،ض ), two for K (ق،ک), two for G (گ،غ) and so on, it's also true that these characters aren't used randomly. There is certainly a logic behind all this.
Take the letters س،ص،ث for instance. If you find ص or ث you can be pretty certain the word has come from Arabic or Persian; while words with س are more likely to have either Sanskrit origins or are recent borrowings from English.
The same is true of letters غ .گ،غ is normally found in words from Arabic or Persian while گ is predominately used for words that have come from Sanskrit.
Gurumukhi, though simple, robs you of this wealth of etymological information and virtually veils the richness of the language and the culture of the people who influenced it in the past.
Unlike Gurumukhi, Shahmukhi doesn't care about short vowels and therefore they are often omitted from the writing. This makes a script a little ambiguous but at the same time more tolerant of different pronunciations.
Take for instance the name of the holy city of Amritsar. While educated Punjabis (influenced by Hindi-Sanskrit) tend to pronounce it [əmrɪt'sər], the better Punjabi pronunciation is [əmrət'sər]. While Gurumukhi tends to favour the Hindi-influenced elites, Shahmukhi spelling امرتسر (Amrtsr) leaves you both the options open.
Finally, and this is where many supporters of Shahmukhi are can't counter, is that it doesn't have the letter [ɳ]. Fortunately, I have come across several works where authors have used O over ں to create a new letter for [ɳ].
Here is a short sentence to illustrate what I have just said:
kʌl sku:l d͡ʒɑ:ɳ vəkt d͡ʒəðð ʊsnɛ zəmɪ:n tɔ̃ bəstɑ: t͡ʃʊkkɛ'ɑ: tɑ̃ ʊsnu: jɑ:ð a:'ja: kɪ ʊsðɪ: kɪtɑ:b faʈɪ: ho'jɪ: æ tɛ kʌləm ʈʊʈʈɪ: ho'jɪ: æ
کل سکول جان وقت جدّ اس نے زمین توں بستا چکّیا تاں اس نو یاد آیا کہ اس دی کتاب پھٹی ھوی اے تے قلم ٹٹّی ھوی اے۔
Here's how it's spelled:
KL SKWL JAN WQT JDD US NY ZMYN TWN BSTA CHKKYA TAN US NW YAD AYA KE US DY KTAB PHTY HWY AY TY QLM TTTY HWY AY.
The underlined words are Arabic in origin. Gurmukhi gives no clue whatsoever to it. The unphonetic words waqt (better spelled as vakt) and qalam (phonetically kalam) give you an idea.