I think most are flying "technically illegally" as of 8th April 2012.
However there is another possibility which I have just read about. Many may have quietly applied the other available derogation that slipped in to the March 30th Regulation:
"By way of derogation from paragraph 1, Member States may decide not to apply the provisions of Annexes I to IV until 8 April 2013".
Annexes I-IV are all of Part FCL and Part MED so presumably this derogation would deal with the N-reg issue, at least until 2013.