I found the answer, and it was the most obvious, of course.
The SMS pause button is configured as the Port 1 Start button in retroarch, so whatever input I bin to Port1 Start does the job. Fortunately this still works if I have the input type as Light Phaser.

@JimmyFromTheBay said in Does Megumi Rescue (Sega Master System) work on anything?:

FBNeo-SMS gets closest - the game starts but the controls are totally wonky. Right and left are back to front and you can't move into the left-hand half of the screen.

The arcade version works properly in FBNeo, i don't know about the sms version (probably nobody tried it), i'll try to take a look soon.

@dankcushions yes! I did the change when I found this new emulator was ported to libretro. At the end I found that the main problem in my lr-genesis-plus-gx performance is the bilinear filter. If I turn it off it's working 58-60 fps with very good sound quality. So as I see it maybe I overloaded my raspberry pi 3B too much, if I'm correct is definitely something to have in mind if you dont have a rpi3B+ or rpi4. SegaCD is working fine too now!