will emulator be allowed

No, for a variety of reasons but mainly because Yuzu isn't accurate enough.

^this

I don't think anybody expects you to merge them into the same category, but a separate category for emulation makes a lot of sense and would be greatly appreciated considering how well it's emulated right off the bat, and how preferable the emulated experience is for many people.
Emulation through Ryujinx is at least 99.9% perfect (they seem to care more about accuracy btw), and Yuzu's almost there as well, if it isn't already. They both get regular updates, especially addressing popular titles like this.
I personally only play through Ryujinx. Some people don't own a Switch, but still purchase the games to legally emulate them for a favorable experience. Even some people who own a Switch still prefer emulation for Dread, because the high resolution & 144 FPS is particularly gorgeous here, including better load times, more accessibility, etc..
I've done quite a lot of testing so far and haven't noticed any differences between Ryujinx and console besides load times, and 144 FPS also doesn't appear to affect anything, apart from one tiny spot where it gets you insta-killed during the EMMI sliding tutorial, but you can simpily press Tab to toggle back to 60 and avoid this, and I believe that EMMI is skipped now anyway. I completed a full playthrough on Ryujinx and haven't noticed any unusual behavior beside that point(yet), even graphically or audibly. While doing my IGT tests for the Discord yesterday, I also didn't notice any accuracy differences between 60 & 144 while actively monitoring the live IGT value. Edit: Both emulators have some IGT pacing issues during cutscenes.
I elaborate on all of this, because I know eventually somebody is going to ask about it.
Anyway, I don't mind too much regardless, but options are nice.

A separate category for emulation would also benefit those, who don't have a capture card (myself included) who wants to run on the leaderboards

I'm pretty sure they've already advised no go for an emulation category in the Discord. That said there are still folks that point a camera at the TV so if you don't have a capture card that might be a viable option.

Maybe in the future, when this game becomes harder to purchase/Nintendo wouldn't care (as much) about the game being emulated. As of now, given Nintendo's reputation on these matters, we should probably hold off on emulator categories, for better or worse.

I personally have no issues with emulators myself, as I ran Gyruss on RetroArch.

Yeah Nintendo especially is on a war path right now with the recent conviction of some people hosting rom sites and bootleg console outlets.