I've never used SQ's thru flights via HKG, NRT, and ICN, but do you even deplane?

I've taken SQ's flight SIN-JNB-CPT and we were not allowed to deplane in JNB. Same situation with ET flights I've taken many times that go via HKG or BKK, you don't deplane in HKG or BKK.

For the OP though, if you do indeed need to deplane and re-clear security in HKG it is no issue at all, you're looking at less than 15 minutes gate to gate in most cases and you won't need to visit a transit desk as you'd already have your continuing boarding pass.