Normally, yes. For instance, if someone has an unhallow spell that somehow affects an entire dungeon level, a detect magic will detect it anywhere in that area (not just where it's centered or placed. Note that unhallow wouldn't normally bypass barriers, but just for this example). The caster of detect magic would have a chance to make a Knowledge (arcana) check, DC 20 (15 + 5 spell level) to determine that it's an evocation aura (and a detect evil spell would detect the area as evil as well, since it's an [evil] spell).
It wouldn't tell the caster that it was unhallow. It requires a DC 20 + spell level check to determine that, but there usually has to be something observable for that to be allowed (like a wall of fire or some other visible effect or interaction).
If the level-wide effect was created by a magic item or creature that somehow emanated or created it, say some unique or powerful darkskull that sat on a magical podium and as long as it was there, it warded the whole level with unhallow, then detect magic would work as above, but the caster would have to be able to see (and have within the detection range) the actual item or creature to determine the abilities or 'identify' its qualities.
A guards and wards causes its entire area to radiate strong abjuration. It has numerous separate spell effects within it, and those will also give off their own auras once within range. Note that some pervasive or large areas of magic can obscure or conceal smaller or lesser auras at a GM's discretion.
