"What is with these disfigured monsters? Her subconscious whispered. Why were there so many of them? Were they all born strange or were they engineered by the great Hephaestus himself?" Can a subconscious "whisper" something to someone?
Not like how you have it used in that sentence. That is more of her just thinking to herself, or ideas forming. The subconscious operates below normal thought. It affects conscious thought and reasoning, but not in a way that the brain could interpret as a whisper. The subconscious isn't really something that a person is aware of.
You could subsitute, "her subconscious whispered," with, "she thought." Maybe that's not what you're looking for but it seems like it would fit ok.
I'd say something like: "What is with these disfigured monsters?" She pondered. "Why were there so many of them? Were they all born strange or were they engineered by the great Hephaestus himself?" Or you could say, Her mind was racing. Or something along those lines. Hope that helps!
I'm not sure what is actually lost if you just delete the entire sentence "Her subconscious whispered."
i agree with the previous two posters... and neither 'her' or 'she' in suggested revision should be capitalized...
I second, maia's opinion. A straight flow of the multiple sentences, or a longer combination sentence, without the "her subconscious whispered" in there will send the same message. If I'm understanding things, correctly, then you're trying to follow your character's flow of thoughts? There are many ways of accomplishing that, but I just let my narration be a running flow of my character's thoughts. All depends on the feel you're trying to get.