Why is it that vertical hallways should be treated differently from horizontal hallways? Especially when people have differing ideas on what constitutes a room? I like multi-floor "rooms", even if the game doesn't recognize them as such. (And I don't use stonesense, either, I just keep a very good image of my fort in my mind.) There is nothing logical about having a bias for mostly-flat fortresses which only have one central hallway.
You're talking about how "players already optimize" in just one particular way, but I certainly don't play that way, and it seems to me that what you are basing this on is, "I play this way, so everyone else should, too." How do you know how many people play that way, and how do you know that people will want to play that way?
Do something for me - rebind your up and down z-level keys to 5 and 0, and play like that for a while. I have a theory that all this obsessively horizontal building is an artifact of people simply not wanting to use > and < to go up and down since it takes a repositioning of the hands to do so.
If they are only playing that way specifically because they want to optimize, then we can optimize for whatever crazy-ass methods we want, and those people are going to do whatever is optimal, anyway, so why should we keep things exactly the same just because this is what people are doing because they feel they have to do it, regardless of how much they like it right now?
Again, I'm not saying that we shouldn't be using nodes, but that we shouldn't be doing strange things like assuming we could never have anything but a single central stairwell fortress design, and punishing any player who designs another type of fort.
Rooms/nodes, however, should be defined in ways that don't have to do with doors. This IS possible, and it is possible by using (hopefully, eventually multi-level) either zoning abilties in the game, or the game being able to naturally infer from narrow chokepoints where the nodes connect.