...or rather, taking into account that you don't know the sex the of the user, I would translate "dear" in Portugues for something more like "Hello", where you don't need to identify the gender. Maybe "Olá" o "cumprimientos" (I forgot most of my Portuguese, so I can't help much).
No, here the word "usuário" is masculine, so doesn't matter if the user is a man or woman. The sentence will not vary in this case.
At least in Spanish we would have usuario (masculine) and usuaria (feminine), so theoretically a woman wouldn't feel represented when addressing her as "prezado usuario". But never mind, thinking of an alternative wouldn't make it look much better anyway.
Well, here we have also usuária and we could say Prezado usuário, Prezada usuária or even Prezado(a) usuário(a). Prezado usuário in places where we can't know if the user is male or female is also acceptable as an alternative to the last one.