I think the question was: Would the items IN the bag show up (i.e. say there was an artifact in there... would there be a very strong aura?).
In general, detect magic can penetrate barriers (see the spell description). So, you would see the aura through a normal bag.
The question lies in whether the stuff in the bag is residing in your plane, or whether it is in some other plane when inside the bag. The description of the bag of holding says that the bag opens into a 'non-dimensional space', rather than specifically saying that the stuff inside the bag is on another plane. In that case, I would say that yes, you can see the auras of items within a bag of holding.