Uh... Not gonna lie, I'm not sure what's causing that problem, and that would probably take a lot more time than I've already spent looking for it. It would also probably mean digging into further code, and I'm not willing to break the game elsewhere for experimentation purposes. It would probably also be a multi-layered fix, not just a flip of a variable or something like that. I have experience coding, but I am not a professional or have expertise in that way, as I am first and foremost a translator. Quick fixes I can certainly do, but that fix would be better suited for another. I apologize for that.
The game has two endings story-wise and around 9-10 H-endings, either from losing important battles, or from subplots.
As long as Nako doesn't engage in any of the H-scenes, you're fine, that just means don't lose boss battles. You can still click on the H-scenes on town that pop up not having to do with Nako, (for example the scene with the black and pink suited people) but if you feel uncomfortable with it, then yes, avoid them. Basically, if your sex level is 1 or higher, you are locked out of the true end. You can view that in the save/load menus once you save.