"Rappaccini's Daughter" is such a loaded story in terms of allegories, metaphors etc. Do you think there's a clear hidden message(s) somewhere or that Hawthorne simply lost control?
I don't think Hawthorne lost control. He was experimenting with metaphor and allegory. There is certainly a reference to Dante's The Divine Comedy and you could say that Giovanni is guided by Beatrice through a world that is both beautiful (paradise) and terrible (inferno). I also see this story as an inverted Garden of Eden. Rather than being banned from the garden, Beatrice is confined to it, thus being shut off from the rest of the world. Rappacini tries to get Giovanni imprisoned likewise, so Rappacini could be seen as God or Satan, or both. So, you can see how this story can be interpreted in multiple ways, even within these apparently obvious allusions to Dante and The Bible. In answer to your question, I would never say there is a certain hidden meaning. That is, objectively speaking, there is no meaning that clearly trumps all others. It is open to interpretation.
You can easily get hung up on comparing the characters to previous literary figures such as Adam and Eve. But these characters are simply not mirror-like repetitions of those previous figures; so, any attempts to derive direct, clear meanings of character motivations and the meaning of the story itself are going to lead to more ambiguity.
I look at this story as being polysemous: having many possible meanings. Part of what determines your own subjective interpretation will depend on the context you place the story in, or what you compare it to. For example, you could argue that this is a feminist interpretation of the story of the Garden of Eden. Beatrice does not “sin” by becoming poisonous. She is forced into it. In the historical interpretations of the Garden story, Eve has more often than not been characterized as the one most at fault. So, historical analysis of Eve's role has likewise forced her into this position of being at fault. Maybe “Rappacini's Daughter” is Hawthorne's attempt to reinterpret this historical bias since Beatrice is innocent. That's a big maybe; it depends on the context.
This story is also about science and life; technology really. Rappacini tries to make Beatrice invincible. Yet, her invincibility cuts her off from the world, from humanity. In fact, her poisonous-ness comes to be what sustains her own life. In a sense, Beatrice is a super-human, technologically advanced. But being so advanced, beyond human, she becomes something other than human, naturally and socially speaking.
Linking technological advancement with knowledge (relating to Eve's desire to know), I see a connection with the benefits and dangers of technology. Even these extrapolated meanings are multiplied and sometimes paradoxical. Science and technology are wonderful in enriching life experience, but there are drawbacks. Social networking (i.e. Facebook) is useful for staying in touch with friends and family. But its mechanism of interaction depends upon a physical separation; another paradox. Beatrice is such a paradox.
I suggest that most stories which appear to be reproaching scientists who engage in radical experimentation, including Nathaniel Hawthorne's "Rappaccini's Daughter" and Mary Shelley's Frankenstein, are really attacking science itself because the authors see that scientific discoveries are undermining faith in traditional religion. The authors appear to be asserting that unbridled scientific research endangers mankind, but the hidden message is that scientific research of any kind endangers mankind because it destroys religious faith. In most stories such as "Rappaccini's Daughter" and Frankenstein there are frequent allusions to God and God's laws. Someone inevitably gets severely punished for attempting to do things that should be left to God and Nature, i.e., challenging God, disobeying God's laws, etc. The battle between science and traditional religion has been going on for hundreds of years. The so-called Scopes Monkey Trial was an interesting sidenote to this epic battle which is far from being over yet.