The use of a hyphen is, however, standard for marking morpheme boundaries, usually not in the context of a phonetic transcription (unless your orthography happens to be IPA, as is the case, rarely, for some descriptive grammars, but then just as normal letters not in slashes/brackets).
I suppose you might end up with a transcription between slashes that has hyphens to show morpheme boundaries, but just like word boundaries, that is usually not marked in IPA, and as far as I know not standard/recommended, and either way not narrowly a phonological (but morphological) question. In doing so, you'd be mixing up several tiers of description and it could get confusing fast.