Or Colbert just doesn't want his personal life spread all over the news. I don't blame him. He'll be back when he's back, and if he want's to tell us, he will. Otherwise, none of my business.
^ This exactly.
Personally if something serious was happening in my life particularly if it was with someone close to me/family and I was in the public sphere I would NOT want to have it splashed everywhere. I don't even like spreading that sort of thing outside of a core group of friends generally, until it's a bit less fresh, let alone a bunch of total strangers.
I'm going to apply occams razor and say this is a publicity stunt.
And I'm going to roll my eyes at the implication that requires few assumptions 
Am I misapplying it? Colbert is a "publicity whore" as part of his character. Stewart, on the other hand, doesn't play a character.
The only assumption I'm making is that Colbert is "in character." That's not that far out there, is it?
When is it appropriate to apply the razor? (It's a serious question, not yanking your chain.)
It could also be something serious though, but why would those be any more likely scenarios?
The problem with your conclusion was that you weren't taking into account all of the known facts and were working solely from the idea that a) show didn't happen and b) people were talking about it. If that was all of the evidence to hand then okay, you could maybe see it as a valid and almost equal option (discounting the statistical precedent for cancelled show/missing work).
The most common reason for cancelling out of work (which is what Colbert and his "character" is, work) is for personal reasons generally personal or family health.
He gets paid to do the show and advertisers pay to have their spots in his new episodes. Two cancelled tapings (whereby people who had tickets to go to the taping were canceled on last minute) doesn't seem like a well-planned publicity stunt.
I think that in this case requires these points to apply:
- Last minute cancellations/ absences from work usually have to do with last minute circumstances (commonly, but not always personal or family health)
- Studio audiences were only notified the day of and not everyone got the memo (suggests lack of planning and demonstrates last-minute nature)
- Advertisers would not have been overly happy about losing type of spot they paid for simply for publicity for the show
- In a publicity stunt Colbert's character would probably have been planting rumours/conspiracy theories, because he's that sort of larger than life character... silence is out of character for him to be "in character"
You added the assumption that the cancellation was planned despite the evidence of it being last minute, which elevated the likelihood of a publicity stunt to the same level as some emergency.
tl;dr: Really what made it less likely was the fact that all of the evidence pointed to it being unplanned so you had to discount that evidence (i.e. add the assumption that evidence was architectured) to make the publicity stunt as likely as an emergency.
Edit: Yes... I know this might sound like "just so" after the fact reasoning... but if it helps I was wrote this before I flipped to the second page and saw that the cause was now known.