What Crown Authority does the HRE have?
Low CA, so it should be possible. I did not mention it before, but the same is true for seizing cities or counties.
Seize trade post : can't against HRE republics, can against independant republics
Seize cities : can't against HRE vassals, can against independant rulers
I would check in the 00_cb_types.txt if I were at home, but maybe it is because you can only DoW independant ruler/republics ? Maybe, as a republic, you can't expand within your liege's realm ? Anyone have any experience to confirm (or not) this ?
PS: I know it looks a lot like a CA issue, but I'm 100% sure the CA is low. At one point, it was autonomous vassals.