This is a good point. I thought about this a bit after first playing KOTORII, and finally wrote some dialogue management code to see how scalable it could be. I think that the saving grace of a nominally more complex system is that it would not be strictly necessary to have unique responses for M/F/DS/LS/etc... in many cases dialogue responses would be identical, but the (non-conversational) *side effects* of the player's choices would be different. So instead of increasing complexity of the dialogue tree, the additional complexity gets offloaded to the force/influence/status maintenance code, which already exists and is (or should be) always running anyway.
Aside from such side effects, much of the dialogue has a limited scope (conversation, quest, planet), and if proper bookkeeping (with respect to force/influence/etc) is done the amount of information that must carry over from one scope to another is minimal. This keeps the state-machine complexity that would otherwise arise down to a much more manageable level... the 'next action' table becomes a (very) sparse matrix and the number of states that must be tracked drops from n^p (n = number of independent dialogues, p for m/f/LS/DS/etc options) to something less than or equal to n*p... the point being that the complexity can grow as a linear function rather than a power function, resulting in much more scalable code.
It seems to me that an NPC that reacts to you based on your actual stats (all simple numbers that are already tracked: the NPC already knows your gender, there are already numbers assigned to force and player level etc) rather than on what your response was to a specific question in a specific conversation on some other planet would seem much more 'intelligent'... the information still gets carried over, in the form of the effect it had on your stats. For quests and plotlines that are more global in scope, more rigorous accounting can be done, but this represents a small fraction of the interactions you have throughout the game.
There is also a reasonably compact fuzzy-logic representation of this type of data that is already used for AI; applying this to management of the PC's state would result in a system that, while not explicitly guaranteeing a specific NPC response, would base NPC's reactions on any number of qualifiers (history, alignment, gender etc) in a contextual manner without excess baggage. It basically provides each NPC with a personality that reacts to your state of being rather than giving them each a list of responses that may or may not be in context.
Much of this is academic in the context of KOTORII, however, since in this game NPCs often forget what you are talking about or what alignment you are right in the middle of a conversation. If the NPC's are just going to wing it regardless of your actions, you don't have to do a lot of state tracking. :/