I think the national authorities are still responsible for issuing AOCs to operators within their territory. The change is that any national regulation (typically based on JAR OPS various amendment status) has been replaced by the hard rules from EASA. Operators with these new AOCs may operate domestic flights within any other EU state. Until HOFO is implemented, EU states may continue with national regulations for offshore helicopter operation as a derogation under Article 6(4) of the cover regulation to 965/2012.
HOFO will create an new subpart in Part SPA, and remove this derogation.
I am uncertain about when this will hit us, but it appears to be soon. The EASA opinion is at the EU commission, and below is some links to more info:
Opinion:
Opinion 04/2015 | EASA
NPA:
NPA 2013-10 | EASA
CRD:
CRD 2013-10 | EASA
TOR and GC:
ToR OPS.093 (a) & (b) (RMT.0409 & RMT.0410) | EASA