It all depends of the challenge you want for yourself. I set these jams as a pretext to explore the skills and methods which I felt were lacking to me. So should you use them too. If you're interested in making a whole game as fast as possible, then you would include the asset creation in the time span. If you only care about programming quickly, then only count the programming time. And, if you care about asset creation, then make the assets, and stop there, or maybe less frustrating, find someone else to integrate them into a game.
You also decide whether you have to be strict regarding the time limit. Personally I have always exceeded a bit.