As far as I remember Ellefson used Peavey back in the time and went over to Hartke when he came back to Megadeth in 2010 (same moment Franko Bello of ANTHRAX got his Hartke deal afaik
). I remember a video of Junior at NAMM 2008 where he was demo-ing stuff at the Peavey/Trace-Elliot booth. Never heard of him using Ampeg.
But, since he has Hartke-Stacks: I don't think he uses Hartke gear for recording at all, just a very good DI and a very good pre-amp. Anything else would suprise me, regarding the studio videos Megadeth posted over the last years.
Nevertheless I think their cabs are suitable for recording. Sure, why not? It's toying around with microphones and position, but why not? I can imagine the hydrive cabs can add some nice colouring to the tone.
I always record DI pre-effect, DI-post-effect and a microphone on the cabinet.