Hmm, Maybe you can config es_systems.cfg to hide them.
<system>
<name>psx</name>
<fullname>psx</fullname>
<path>~.emulationstation\roms\psx</path>
<extension>.zip .PBP .pbp .BIN .bin .IMG .img .ISO .iso .ccd .CCD .nrg .NRG .mdf .MDF </extension>
<command>..emulationstation\retroarch\retroarch.exe -L ..emulationstation\retroarch\cores\mednafen_psx_libretro.dll %ROM%</command>
<platform>psx</platform>
<theme>psx</theme>
</system>
On the <extension>
just delete the .bin .cue or .pbp .iso
Basically whatever you don't want to be seen on the game list.
This is my config from my windows Emulationstation