IPA is not typically used for transliteration. It is often used for phonemic transcription, and sometimes for phonetic transcription.
(Phonemic transcriptions are conventionally enclosed with slashes, and phonetic transcriptions are conventionally enclosed with square brackets.)
I am not an expert on the IPA, but based on my experience reading linguistics articles and things like that, I would say that the symbol ∅ shows up mostly in descriptions of rules or sound changes (like "f > ∅ /V_V"). I have never seen it used in the context of phonetic transcription of an utterance.
The symbol ∅ does not even seem to be part of the International Phonetic Alphabet, techncially speaking: I can't see it anywhere on the official IPA chart as of 2015. Wikipedia lists some other uses of the empty set symbol in linguistics.
There is no IPA police that will arrest you if you transcribe the pronunciaton of light as "[ˈlaɪ∅t]", but I don't see the point of doing this. A phonetic transcription is not supposed to indicate information about the spelling of a word.