Unfortunately, it doesn't seem to affect cutscenes.
I've since modified the latest source for switch toolbox to support saving/replacing files in PKG archives.
Replacing actors\characters\samus\models and morphball\models can be done directly now.
Export samushyper and morphballhyper and replace the other suit models with them, and save.
Oh really? I was using that tool initially but had no way to modify files in it in the previous version.
Does this method still not work for cutscenes though?
What I have found to work for cutscenes is to edit the save file (common.bmssv) directly. I renamed one of the suits to 'HYPER'. Although this replaces that suit's functionality too so I lost gravity suit functionality when renaming the suit to 'ITEM_HYPER_SUIT'.
What's also cool is that you can rename beams to enable the hyper beam (ITEM_WEAPON_HYPER_BEAM). Although this prevents aeion abilities from being used as well as the grapple beam so you might not be able to get everywhere but it's still cool nonetheless.
This lets you get to the end section.. Where your ship model doesn't exist (trying to leave this area again seems to crash the game as I get stuck on a black screen). You can also destroy the EMMI head armour but unfortunately you can't kill them with the hyper beam.
Can it be done and how on Yuzu emulator?
Yep, you can do this in Yuzu by putting the config.ini in the following folder: %appdata%\yuzu\sdmc\atmosphere\contents\010093801237C000\romfs