As lesser undeads like skeletons or zombies are mostly made by magic I'm wondering if detect magic can be used as sorts of "detect undead in your view". Thus you see a pile of bones ahead of you and the first thing you do is you cast detect magic and see "magic aura thus very likely skeletons in disguise.....where is the club to smash them before they rise?"
So can detect magic be used for a lesser replacement of detect undead in such cases?
No, it can't. Animate dead and similar spells typically have a duration of instantaneous. This means the magic is only present at their creation (and for more powerful spells/spellcasters, an aura may linger for a time). After that, the negative energy has already infused the creature and made it undead - this is a "natural" (stretching the term quite a bit) state for an undead creature, and requires no ongoing enchantment to keep it functioning.
A lot of confusion on this issue stems from the fact that the only way mortals (read: your PCs and the vast majority of NPCs) can manipulate positive and negative energy is through magic. But a dead body infused with negative energy in other ways can become undead without any "magic". A deity capable of manipulating negative energy directly can just push the energy into the creature. A place where lots of dark things have happened can naturally attract negative energy, and people who die there may rise as undead. Some undead can "infect" living targets with negative energy carried by a natural vector, like a disease or poison (like plague zombies). None of these require any magic to create the undead.
Basically, animate dead just "starts the engine", the creatures can "run" without any more magic.
