How can Southern blotting be used to establish gene copy number?
This method is commonly practiced. Atleast I see the people working with zebrafish transgenics using it.

When you shear the genomic DNA or do a restriction digestion, you are likely to get fragments of different sizes. 
It is highly probable that the two (or more) locations harboring a copy of the DNA element are a part of fragments with different sizes. So on the blot you'll get two bands.  

But as I said this test relies on probability that the two fragments are dissimilar in length. Therefore, southern blot should not be considered as an absolute test to determine copy number. Inverse PCR, FISH, etc can be used to determine copy number.