The default size of the window is hard coded. You could search the string in the executable with a hex editor and patch it.
But the better solution would be this:
create a small shell script in S: (lets call it NS) containing the command
newshell con:0/150//300/AmigaShell/AUTO/CLOSE
then set the S flag (protect s:ns +s).
Now you can open the execute window and enter ns for a new shell window. Even shorter than CLI.
Make sure that S: is contained in your path before LoadWB is called. Maybe you have to move the script to C:. Workbench is very restrictive with its path setting.
Bye,
Thomas