I’m thinking about getting a raspberry pi 3 because they are very cheap and I want to know if I can use it for (emulator) runs. It uses mupen64plus which I see is allowed and it is also a Linux system.

it’s not allowed, read the emu rules under “Rules” at the category you wish to run

Well yes it does run Mupen I'm really not sure I practice on Retro Pi but IDK

Listed emulators are on rules

We know but Retro Pi runs on Mupen 64

Yes, it would be allowed as you’re running through mupen64plus.

you can get mupen on phones, but that is stilled banned.

No, RetroPie isn't allowed.