One QR Code or Many QR Codes for Same Wine in differently Sized Bottles?

The answer is: It Depends!

If you are using the standard non-gs1 qr codes, then you would only need 1 code for all bottle sizes.

If you wanted to use the GS1 codes and your different bottles have different barcodes you have get one code each.

The decision to get GS1 Codes also depends on how long you expect your product to be on the shelf. 

Please take a look at the following article for more information:
e-label - Editor - QR Code - GS1 Digital Link - System Logic and Facts that are Good-to-Know