EmuDeck uses EmulationStation, in which I’ve seen a lot of controller-related problems. Controllers working in the menu but not in the emulators. Controllers working in the emulators but not in the menus.
For a dedicated emulation machine, I’ll once again shill for Lakka, that boots LibreELEC directly into RetroArch without EmulationStation, and has bootable installers for multiple configurations of x86_64 machines and images for loads of single-board computers.