Well I think it shouldn’t be a problem really, because it is not going to be very likely that you will duplicate an object and leave it in the same place over and over again, with each object. When you’re modeling you tend to have very good control of your model, enough to know you haven’t made a duplicate of all the vertices and left it in the same place. Sometimes it tends to happen that you extrude and you need to undo and you don’t undo enough and you leave some duplicated vertices, but that tends to be very noticeable since it introduces shading errors and it makes you go in and see what is going on. So I wouldn’t worry too much on having this problem, you’ll get the hang of it as you model more and more.
