Yes, if you change the CPU architecture, the container has to be emulated. And yes, it can affect performance and sometimes it doesn’t work at all.
Docker Desktop is for development and emulation helps you so you don’t have to buy another computer for the other architecture. If you want to run an application in production, run the Linux container on Linux on the right architecture. Depedning on what the application does, it could run emulated in production, but I wouldn’t do that normally.