If you have a genuine question that is not answered by any of the course literature or website then by all means contact the course in question.
If there is a generic email address or online form for questions then use that, it will most likely be answered by a member of support staff who will hopefully be able to help you.
In my experience (UK, master's courses), contacting academic staff is discouraged simply because there isn't really anything that an academic would tell you that an member of support staff could not - and if there is, then they would forward it on form you (thus keep busy academic inboxes clear!).
Of course, this doesn't necessarily mean you would be penalized (unless it explicitly says not to on the website etc.) for searching out the course director's email address and contacting them directly. But be prepared for a longer wait on your reply and the possibility of an answer from someone else.
On the topic of whether personal contact with an academic would increase your chances I have this to say: an enquiry email for unlikely be of much help in enhancing your application, being a former student, friend, associate etc. could possibly help your application (rightly or wrongly) and would give you more reason to email them directly. Unless you are acquainted, emailing a course director is unlikely to enhance your application (assuming that all the lovely things you want to say about yourself aren't in the app already!).
Again, this is from a UK, taught postgraduate perspective. Conversely, many research degrees recommend contacting an academic directly first. I am not familiar with etiquette in other countries, but assume it will vary.