I’m that much of a sad act ( and had nothing better to do) that I counted the time between a train entering the crypt and one cresting the lift hill at 32 seconds.
Has to be on two.
With the duration between the crest of the lift and entering the crypt only being around 30-35 seconds, that would make for a dispatch interval of about 67 seconds at worst… which could honestly put it on 3 unless that’s simply the quicker dispatch interval out of 2 trains.
I’ll admit that I’d be absolutely stunned if a 3-train Thirteen had a queue as long and slow-moving as you describe, though… even with high quantities of Fastrack and RAP, I’d expect 3-train Thirteen to be a bit more of a queue muncher than that. 1 hour to get to the vending machines sounds painfully slow…
Here’s a handy hint for when you get to the station. If the ride is on 2 trains, you should see a gap between a train leaving the station and the train behind re-entering it, and you won’t stack at the end. I rode it last year when it was on 2 trains, and for some idea, there was a gap in the station, and when I was about midway up the lift hill, I was seeing the train in front emerging from the crypt onto the final brake run.
Coincidentally, I also queued 105 minutes for it that day… Thirteen gets busy on reduced capacity, it would seem!
EDIT - It would seem as though Alton Towers’ own official POV would peg the dispatch interval I describe at around
1m 18s, at a rough guess, so I’m going to take a stab at the ride being on 2 trains based on the info you’ve given: