It was highly recommended while traveling in Guatemala and Nicaragua to bring your own pad lock, since the keeper of the hostel had extra keys to pad locks that they lent you. Friends of mine had a significant amount of money stolen out of their bags because they used the hostel pad lock rather than their own. Is the situation in Cuba such that pad locks are even used as a private entry security feature, or are the locks just key in door handle locks?

To answer your questio a little more directlty: In a situation (any situation) in which a padlock might be required - bring it! Keys to accommodation will be of the key-in-door-handle type. Be assurred that there are (many) copies.
Padlocks are great for appearance, and yes you should use them in Cuba or anyplace in the world. But razor blades are prevalent in Cuba as elsewhere, so if you have a canvas or leather bag, each time you return to your room always look for slits in your luggage along a seam - just big/long enough for a hand to slip into your bag.