This looks very like a problem I encountered some time ago running the closed source 3DO emulator "Phoenix Project", and similarly the open source "FreeDO" project that it was forked from. I narrowed it down (also using strace, IIRC) to these programs repeatedly opening and closing the /dev/input/event* files, and that being weirdly slow. I made a seperate little test program just to open and close those files to confirm it. It was only slow on my main desktop machine; while on my lesser-powered laptop, running a practically identical Arch Linux setup, those file operations were quick and the programs ran fine. None of these programs use SDL. I couldn't/didn't progress any further then, but it's good to find some pointers here for further investigation (ie. the libinput issue).

Funnily enough I'm pretty sure I played Papers Please on this machine at length without problems but I think that was probably the Windows version through Wine.