Hi i used to play on an emulator SMB1 and SM64. i bought a nes classic mini for smb1 and figured out after inspecting the device and searched a little bit in the internet that i can play n64 games and gameboy games and what not. Will Speedruns on this device be Legit?

Don't know anything about the method, but since it's still emulation, it's not going to be any more "legit" than your previous runs. Supposing that this method is unofficial, there will be no difference, and it may be worse since it may be more difficult to verify the emulator accuracy using such an uncommon method.

You’ll have to ask the community, but some times the modding of the NES Classic to play ROMs is banned because it’s considered console modification.

For what it’s worth, the NES Classic will also run slower than regular consoles or computer emulators, so there is zero reason to ever use it if you’re already using an emulator on your computer.

i dont mind if this is slower but is way more fun for me to play like this. I still dont know if this will be legit or nah. when i have negative effect while useing this in form of timeloss it should be legit or nah?

I already answered in my very first sentence - “You’ll need to ask the community”. They’re the only ones that can tell you if it’ll be allowed.