A year and a half later, there is still no solution to fix the sound in the beebem.
Here's what we have so far:
The sound does not work at all or sometimes only works for a few seconds, if we turn it off and on again in the menu.
I looked in the src folder and saw that a large portion of the sdl.cpp file contained sdl sound entries, but I'm not skilled enough to determine where the problem is.
In the same emulator running through teminal windows inside desktop raspbian, the sound works ok.
I also read that support for alsa audio driver needs to be added but I don't know if anyone has done this successfully and how.
Another problem is that the emulator crash (with some GTK error) when using the floppy requester in the internal menu but this can be overcome using the command line options.
For now, the lack of sound is the biggest problem and I hope someone will know how to customize this emulator for retropie.
I have contacted the author by email regarding these issues but for now I have not received an answer.