yeah www.aldostools.com has a way to take the dos window down but it only run in the emulator itself not in epsxecutor, I think that really don´t care much if u have the window or not, but other way maybe execute the program minimized or something I don´t know but really try something
Download Aldo's Speedup Process, install it and run the following command line:
C:\ePSXe\SpeedUp.exe /x /q C:\ePSXe\ePSXe.exe
Change the directories for the ones you use and that's it. If you want to, you can add more options to the command line to free memory, close other programs, and other things. Look in Aldo's site for more information.