That depends.....on low calories, longer duration/intensity cardio can very well lead to overtraining, thus CNS taxing and muscle wasting.
I believe unless you are an endurance trainee, this would lean somewhere towards fact for most. How many long distance runners do you see that are muscular?
In the end, the body will use whatever substrate is available to it. It is easier to use glycogen up(think of hitting the wall??), than to mobilize FFA's for any intense exercise. I.E...HIIT type cardio. In fact, it cannot do so.