It may very well be ok, but I personally try to stay away from shell=True. Unfortunately I can't really say why... But somehow I have in mind potentially weird behavior (maybe related to command-line parsing? not sure)
So... not sure if it's relevant here, but given that we don't properly test Theano under Windows, are we confident that it's safe to use shell=True under all environments?

Side note: any idea why it won't find it with shell=False? It's not just a PATH issue?