I don’t think that the Houthis have S-400s (and I can’t imagine that Russia has been providing them to anyone in the last couple years, given as how they have a shortage themselves, and it’s probably one of the more-critical shortages that they face).
I can’t find any reference to the Houthis having them online, at any rate.
The New York Times stated that this was specifically asked the Pentagon, given the phrasing of their announcement and got a no-comment. It’s certainly a good thought.
https://www.nytimes.com/2024/10/17/us/politics/houthis-strike-stealth-bombers.html
EDIT: Reading the above, maybe the situation is basically both of the two guesses here combined.
It’s a message to Iran, and the reason that the B-2 specifically is involved in that message is because it can drop very large bunker-busters, which could presumably penetrate Iranian facilities.