Could you please help me to understand how much space in a node does an empty block with no extrinsics/transactions take up?
The empty block with a maximum block size of 1MB is not going to be 1MB in most cases (unless you have custom runtime logic which is adding data, which I doubt is the case).
Therefore, the empty block is likely to be small in size, maybe something around a hundred or few hundred bytes.
We are running a testnet and this is the data it print below. Most of our blocks are empty at the moment so hopefully this helps.
You can find similar charts like this by going to the Apps UI and clicking on "Explorer" and then "Latency". One of the diagrams should show the blocksize of the last X many blocks.