Ordering a bottled water & two Pepsis is hardly evidence of a second guest and/or perp. It is evidence of someone who might like two Pepsis with his meal or wants to save one for later.
I generally stay at Courtyards on my business travel. I get two bottled waters and a Diet Coke every time I check in. I fear both dehydration and a lack of caffeine and the two are almost certainly connected.
People who travel a lot (and this guy might be that) fall into patterns that probably don’t make a ton of sense to a neutral observer.
Reading too much into this stuff will drive you nuts.