...which is of course zero.
...which of course is zero.
Which one is preferred?
I don't think there's much difference between the two. It depends on which word you wish to stress more: which or zero. (Incidentally, I would set it off with commas, but that is a matter of taste.)
This saves all the emphasis for the final word zero:
... which is, of course, zero.
This puts the emphasis on which:
... which, of course, is zero.
There is no difference in meaning, only in dramatic effect. The effect is greater if the sentence is spoken; if it is written, the effect is vanishingly small.
I personally would prefer
... which is of course zero
if I wanted to stress is or zero.
... which of course is zero
to me sound more like
there is no doubt, of course it is zero
putting more stress on of course.
This might be quite subjective.