An interpretation, potentially correct, potentially not:
Here in my part of the world, the culture is allergic to direct communication. Something about religion, "contention is of the devil," yada yada. It sounds to me like your partner is asking a "direct" question that is not actually what she wants to know.
In other words, "Did you eat that pizza?" is more like "Why did you eat that pizza?" Or even, "I was really looking forward to eating that piece of pizza myself but I forgot to tell you so, and now it's gone and I feel frustrated that I can't eat it, and guilty at the same time because how could you have known that I wanted it if I didn't tell you?" So asking why directly invites vulnerability. Potentially, as I said. This is just a theory.
Where I'm from, people feel a lot of shame for even getting frustrated—nevermind angry—because they think feeling that way is a sin. So they talk around this feeling and never confront the fact that they might be displeased about something. The pizza question reminds me of this.
"Why do you smell like alcohol?" makes me think of the question, "Have I done something wrong to drive you to drink, are you going to end up in the gutter like Edgar Allen Poe, will you die of tuberculosis like Mozart, I don't want to lose you, what is going on?" But all of this is vulnerable, and shows your partner's judgments about drinking. She may have any number of reasons for wanting to hide these judgments—an indirect or rhetorical question is one method of hiding them.
I dunno, maybe this is helpful or maybe it confuses things. Either way, I share your frustration, and have a tendency to snark pretty hard unless I manage to stop myself.