I am not any linguistic expert , but my basic understanding is that – People who spoke Tamil never used those syllables in early times. One place Hart points out that probably Tamils didn’t like the pronunciation of the Sanskrit words and had to use Tamil words for words of Sanskrit origin eg. Veda–>marai etc.
This was during sangam age. But Tholkappiyam (atleast the basic structure was written in about 100 bc) was written much before this age which defined the grammar for the coming age .
This is some thing like the tribal in ‘god must be crazy’. He uses sounds which we can never incorporate in most of the languages.
Early Tamils were unfamiliar with the Sanskrit tones and hence when the scripts were formed for their own script they didn’t accommodate the scripts for these syllables.Tamil is oldest available Dravidian language most probably had pre literary culture before any Indo aryan language could penetrate.The fact that Tamil is from diff language chain and sankrit being a diff language chain might have been the biggest contributing factor.(Except for Tamil all other Dravidian language literature started under influence of Sanskrit so cant be taken in the above context)
Even in 10-12th century Kamban chooses to use ilakuvanan instead of lakshman. We can also see swami changed to sami even in these days.Probably if we go deep interior rural tamil nadu we might find people having difficulties pronouncing the sha and jhas.
on a lighter note I remember Senthil pronouncing pusham as puipam in some old Tamil movie.