Why refrigerate bagels after shaping dough? I've noticed that recipes for bagels call for a refrigeration period after shaping. Why does it matter if the refrigeration is done after shaping? 

The shaped dough takes up more space in the fridge so it's not ideal. 

At least with respect to pizza dough one source says that:


  Doughs that are shaped and proofed after a slow, cold fermentation
  demonstrate noticeably better flavor and better structure.


So why shouldn't we refrigerate the bulk dough and shape afterwards?
It doesn't matter as far as rise or flavor is concerned.  You can cold rise the dough, or the shaped bagels, or both.

However, the advantage of cold-rising the shaped bagels is that the cold dough is easier to peel off and dunk in the boiling water than room-temp dough is.  Bagel dough tends to be sticky and soft, and it's challenging to avoid stretching the bagels while dunking.