As Pyro has stated, and as supported by some performance test comparisons, the AH Spitfire Mk. IX has a Merlin 61 engine.
To the best of my knowledge, all of the Merlin 61 aircraft were built in 1942 and carried the C wing with .303 guns. These included the first 100 or so Mk. IX aircraft which were actually modified Mk. Vc airframes. The C wing was standard on the Mk. IX until after the Merlin 61 was phased out and replaced by the Merlin 66 or 70.
Spitfire C or E wings had a pair of closely-spaced gun tubes in each wing, which were originally intended for a pair of 20 mm cannon. C wing aircraft (e.g. Mk. Vc) usually had a cannon in each inboard gun tube, with each outboard tube blocked off, and a pair of .303 guns in the outboard part of each wing. E wing aircraft (e.g. Mk. IXe) had a cannon in each outboard tube, and a single .50 gun in the inboard tube.
Furthermore the E wing aircraft generally had the enlarged rudder as used on the Mk. VIII and pictured below on a Mk. XVIe.
Spitfire LF Mk. XVIe Note enlarged rudder and cannon in outboard tubes.
Problem:
The AH Mk. IX has a Merlin 61 and the short rudder. This means it is an F. Mk. IXc. But a C wing should not have a 0.50 cal option. Therefore the 0.50 cal option should be deleted in the game.
The E wing was used only on LF Mk. IX (Merlin 66), HF Mk. IX (Merlin 70), and Mk. XVI (Merlin 266). If HTC want to put 0.50 cal on a Merlin Spit, they need to model one of those.
Disclaimer:
The Mk. IX/XVI was probably the most varied Spitfire mark. There are so many combinations of armament and engine type and airframe details that almost any combination seems possible. I don't think it would be any great chore to field-modify a C wing Spit to carry a 0.50 cal in the vacant gun tubes. But I've never seen any report of this occuring.