No Merlin 61 Spit IX carried .50 cals.
The Spitfire Mk IX in AH represents the earliest version from 1942. The Mk VIII, which in AH has a Merlin 66, can be used in place of the Spitfire LF.Mk IX from 1943. The Spitfire Mk XVI was only ever powered by a Merlin 266 (The Packard built version of the Merlin 66) and equipped with a "e" wing which had two 20mm cannons and two .50 machine guns.
Interestingly, the AH Spitfire Mk XVI is actually a Spitfire LF.Mk IXe. You can tell by the critical altitude of the engine. A Merlin 266 had a critical altitude about 1000ft higher than a Merlin 66 and the Spitfire Mk XVI's power curves match, exactly, the power curves of the Spitfire Mk VIII in AH. No Spitfire Mk VIII had a Merlin 266, so....both are powered by the Merlin 66, making AH's Spitfire Mk XVI actually a Spitfire LF.Mk IXe.
That is fine, to be honest, as the Spitfire LF.Mk IXe and Spitfire Mk XVI came off the production line mingled together, the mark being determined by which engine was installed.