Book is 'away at an abbey'? Do we ever get any other explanation than that?
Not specifically no, but take note that the first time Serenity visits a core world, Book conveniently finds an excuse not to be there. Just another hint about our mysterious shepherd.
Does Mal protect River and Simon from the goodness of his heart or to stick 2 fingers up to the Alliance?
Probably a bit of both, but with the former hiding underneath the latter. Mal may not be a nice guy, but he is a good guy. He'd just rather not be.
Did we get to the episode yet where it is revealed that young Simon Tam is secretly Zac Efron? I forget which episode that is.