Phonetically many words do not make sense anyway, the English language is pretty stupid when it comes to this. There are roughly 220 sight words that are imperitive to learn in order to begin reading fluently on a basic level. These need to be learnt mainly by sight. Words like you, what, which, know etc etc.
The program was founded in 1982 and i have never heard of anyone, dyslexic or non-dyslexic experience anything detremental to their learning.
How long term do you mean?