Per default I would see that scene playing out off-screen. The sex system mechanics already work pretty fine without the player actively doing anything, so having a sex scene entirely off-screen shouldn't be that difficult.
But considering that the game now works in time increments of one hour, it would also be possible to show some kind of notification for an ingame-hour saying that two characters are getting it on right now. The player should then be allowed to peep and/or join in if they want to (starting a regular sex scene with the two characters).
I would not do this as a modal popup event the player is forced to interact with, because that might get quite annoying in the long run (especially if the player aims to construct a "swinger club" scenario where everyone is constantly fucking - something I would really enjoy, by the way). I would rather do it as an icon in the character list or a toast notification which can be easily ignored if the player does not care right now.