I had a similar issue (not wanting the splashscreen to be displayed every time you run an exe).
One way to resolve this is to delete the splash.png from the installation folder - rather than do this manually I do this in my primary m-file, it does mean that the first time the exe is run the splashscreen is displayed, but subsequent times it is not, so for my purpose its an acceptable work around:
[status, result] = system('path');
installpath = char(regexpi(result, 'Path=(.*?);', 'tokens', 'once'));
splashpng = fullfile ( installpath, 'splash.png' );
if exist ( splashpng, 'file' ) == 2
delete ( splashpng );