I don't think any production variants of the F IX ever had the E guns There were a great many experimental weapon configs, so prototypes may have had such a configuration.
I found this on another site:
According to the official Pilot's Notes (3rd edition, 1946):
"INTRODUCTION
1.(i) The variants of the Spitfire IX,XI and XVI are distinguished by prefix letters denoting the general operating altitude or role and the suffix letter (e) is used where .5-inch guns replace .303-inch guns. The aircraft are all essentially similar, but the following table shows the main features that give the various versions their distinguishing letters:
F IX Merlin 61; 63 or 63A; two 20-mm. and four .303-in. guns.
LF IX Merlin 66; two 20-mm. and four .303-in. guns.
LF IX (e) Merlin 66; two 20-mm. and two .5-in. guns.
HF IX Merlin 70; two 20-mm. and four .303-in. guns.
HF IX (e) Merlin 70; two 20-mm. and two .5-in. guns.
PR XI Merlin 61; 63, 63A or 70.
F XVI Merlin 266; two 20-mm. and two .5-in. guns.
(ii) Merlin 61 and 63 engines have S.U.float-type carburettors, but on Merlin 66, 70 and 266 engines these are replaced by Bendix-Stromberg injection carburettors.
(iii) All these marks of aircraft are fitted with Rotol 4-bladed hydraulic propellers and on the majority of aircraft the wing tips are clipped
http://folk.uio.no/hungnes/avia/spitfire/mkixvar.htm So according to the offical pilot's notes, the F IX never had 50 cal guns fitted.