They sure can, but if you want to use masterbase provided by this site, you should first make the double faced cards in your magic workstation showing only the front side with mana cost. This can easily be done by seleting the double faced card, right clicking on it, then clicking view/edit record. There you will find all the information about the card which you can modify. After doing so with cards you want to play, don't forget to save masterbase. And be aware, after updating the masterbase by downloading a new one, you will lose the information.
There is another option. You can create separate cards tools, and card creation center. That will allow you to have the other side in your masterbase, but that will take more time, since you'd have to create the cards manually. That's pretty much it, I made double faced cards playable in MWS, so can you.

Good luck.