How does repeatedly freezing and thawing antibiotics decrease their antimicrobial effectiveness?
As indicated in the comments, freeze-thaw cycles should not affect molecules of size of typical antibiotics. Freeeze-thawing may affect colloids by disrupting their structure. Also, the effect would depend on how fast a sample was frozen/thawed etc (slow freezing would cause rearrangement of molecules and crystallization of water whereas rapid freezing would result in vitrification of water.)

The popular lab practice, in my opinion, would have perhaps arisen because it is better to keep the stock stored at the appropriate temperature (frozen) for longer life. Repeated thawing of the stock would definitely increase its chance of degradation because of mishandling and even otherwise. Therefore, it is better to aliquot smaller volumes; even if you have forgotten to keep it back into the freezer you'll end up losing only a small amount. 

 

Not related to your question but this is an interesting fact: freeze-thaw cycles promote molecular assembly of RNA into higher order structures (ref).