There is really only one case in which I scuttle labs, and that is when I built two civic labs to research ice and/or volcanic colonization. These technologies, and a few others at the lower tech levels, remain accessible after the labs are scuttled, letting me continue to colonize these worlds while putting all my logistics space towards factories and military labs.
Otherwise, later on, you should keep all your labs operational. If logistics space is actually so important that you need to consider this, your empire is probably so small that you're not even ready for 8 civic labs yet anyways.