I found a workaround:
I added a .scm-File to the root aof the scummvm-games-folder.
For atlantis i have the atlantis.scummvm-file insidde the atlantis-folder and a atlantis.scm-file outside that folder.
In es_systems.cfg i changed the command:
<command>RetroArch\retroarch.exe -f -L "RetroArch\cores\scummvm_libretro.dll" "PATHTORETROGAMES\retro\ScummVM\games%BASENAME%%BASENAME%.scummvm"</command>
and changed the extension to scm.
<extension>.scm</extension>
This means EmulationStation sees the .scm-file as the rom and adds it to the gamelist without annoying subfolders.
When starting the rom, wo don't care about the fake .scm-file. We grab only the basename and assume there is a folder with the same basename with the scummvm-file inside it.