Warning is not issued to console if you call mkdir with output values to capture the msg.
[ status, msg ] = mkdir( 'someDir');
This is described in doc for mkdir: "If the number of output arguments is 1 or less, it also issues a warning that the directory already exists."
So, no warning if you provide the args. This also works if you provide placeholders:
[ ~, ~ ] = mkdir( 'someDir'); % ignore outputs.