Have you seen the info on this site (Home Page > FAA Bases 1939 to present day)?
RAF Aboukir is listed as 'HMS Nile II'. I don't know if there was another HMS Nile. Another shore base nearby was RAF Dekheila / HMS Grebe (near Alexandria).
I too have been looking for info/station diaries for this area for 1939-40, and this is the most detailed I have come across. (see my post on 30 Sept 2014 [Helping researchers>RN research archive projects need your help]).