I'll be interested to see what Mathworks people will answer (maybe tomorrow). If I had to place a bet, I'd say that it is for backward compatibility with a "feature" that was a bug but that might have been exploited by people.. who could therefore disable the warning and use a "silent" backward compatibility.
The doc indicates a change in the behavior of UNIQUE and the support for a 'legacy' option. Also, the version of UNIQUE called with cell args is available as an M-file
C:\Program Files\MATLAB\R2012b\toolbox\matlab\ops\@cell\unique.m
which looks quite experimental/transitional.