Ok, here we go.
Create a file called cps3.ahk with the following in it:
setworkingdir, path to cps3 emu
run cps3 emu command
$esc::
soundget, volume
soundset, 0
send {esc}
sleep 3000
soundset, %volume%
exitapp
Put in the path to the emu where indicated. Replace
cps3 emu command with whatever you would type at the command line to run it, but instead of a rom name, type %1%. I've assumed this emu exits by pressing escape, if not, you'll need to change
send {esc} to whatever it should be sending. I've set it to wait 3000 ms before turning the sound back up and exiting the script. If this is not enough/too much time, just adjust it until it seems about right.
Add these to the appropriate places in your mame.cmd
if "%2" == "C:\emus\otheremus\cps3\roms" goto cps3
:cps3
cd C:\Program Files\Autohotkey
autohotkey.exe C:\emus\cps3.ahk %1
exit
As always, change the file paths to your own.
Let me know if this works for you!
As for the command line showing up when you launch zinc, I don't think I've ever had that problem with Zinc and Mala. Are you sure you have Dos Window State set to hidden on the main Mala config menu?