Answer: First, here's a bit of terminology. The abbreviation "mss" stands for "manuscript". A manuscript is your work whether it is a novel, a script, a non-fiction book, etc.
To most publishers, the phrase "Does not accept unsolicited mss" simply means that you may query but you cannot send the entire manuscript. Too many writers believe that if they send their work (without first sending a query) that their chances are better. Wrong. You should never send a complete work to someone without them first requesting it. It will only wind up deleted or recycled; never read.
In other cases, the listing may state this because the agent or publisher will only take referrals from current clients, or the publisher will only take agented submissions, or they may be closed to submissions for awhile.
How to tell the difference
If a listing that states "Does not accept unsolicited mss" doesn't specify that they only take submissions from certain people, then chances are, you are free to send a query per their guidelines. When in doubt, don't hesitate to email the listing and ask. Many publishers and agents will appreciate a quick question rather than getting material they don't want.
In any case, following submission guidelines is imperative when submitting.