Yes, @EXEC in the config.ini file works fine ever since it was implemented way back when. You were probably thinking of SITE EXEC in FTP which I don't think Hijack has ever had. I think that this syntax still applies today. I am actually using a line like this to run a shell script:

;@EXEC_ONCE /bin/bash -c "/usr/local/bin/start_empire 10 &"

Works great.