They certainly can be in **a** game, just not this one. And it's not about not inviting people's bitching, because the absence of those traits will also cause people to whine. In fact, no matter what you do, someone will be dissatisfied with it. So, the best thing developers can do is tailor the game to both their personal tastes and what's appropriate for the story they want to tell.
And speaking to my taste, I just don't like harems or incest in stories.
Generally speaking, the MC convincing five women to love and be monogamous solely to him stretches my personal suspension of disbelief a tad too thin in most cases, outside of more shlocky scenarios. It CAN work, but it doesn't suit the tone I want for Pale Carnations.
As for incest, it's usually cheaply done in my opinion, without any sense of weight to the taboo. To do it in a way that I'd be satisfied with, the scenario would have to support it and go in a direction I have no desire for it to go. Plus, I just don't find incest hot, even when done up like a steamy angst-ridden French movie. I did like Dreaming of Dana's approach to it, with the game's ultimate goal being to find a beard to conceal your relationship with your sister. For me, that sold the "society won't accept this" bit that most stories nominally bring up a couple of times but don't ever actually factor into the plot, but I'm also just a sucker for procedural elements.
Anyway, point is, a VN should be more than the sum of its tags, so nevermind what the player wants. Convince them of what you want.