Did Maester Aemon take the Night’s Watch oath? And which oath would take precedence if they ever came into conflict, the maester’s oath or the NW oath?

Yes, he did – that was the whole point of why he went to the Wall, to belt-and-braces the idea that he was in no ways eligible to King. 

As to the two oaths, they’re acctually quite sympatico: both oaths require celibacy, abjure any right to political power/landholding, both institutions are supposed to be neutral in politics, etc. 

The only situation I can see the oaths conflicting is if some foreign power were to seize the Wall – it might be the case that the maester would be bound to serve them, while the Night’s Watch oath demands loyalty to the Watch above all. But that conflict hinges on whether the maester is considered to serve at the Wall itself or serving the Night’s Watch as a collective institution; only the former would give rise to such a conflict.