The same thing happening to me since launch. Not just the cutscenes freezes and audio desync, but even the main menu video get speed up when you boot the game, the BEYOND lags when it shows up, and the animation lags when you press "A". I tested on firmware 19, 20, 21, Atmosphere in different versions, all modules off, restarted Switch a lot of times, downloaded the game from different sources and sizes, oveclocked the CPU/GPU, recreated emuNAND (always used SD file since people say is more easy to deal with), used another SD card, nothing fixed these freezes or audio desync, or even the stutters in portable mode. I finished the game that way, searching for the cutscenes on Youtube.
Yesterday I find this post, tried to create a emuNAND with SD partition option, installed firmware 20.1.5, Metroid Prime 4 with update 1.1.0, emuiibo, Mission Control and Tesla modules active, with default clocks and the game runs smooth like butter. Not a single freeze in cutscenes or even a single stutter in portable mode! So I believe emuNAND in SD file is the culprit here. I'm surprised that Metroid Prime 4 was the only game that I played in Atmosphere since I have the Switch OLED, that give me that kind of performance issues. From now on I will always use emuNAND in SD partition mode.