I think approaching nair, when a marth will just nair into an opponent's shield or try to cross it up with it, is not a very effective option as well. It's easily avoided and can be taken advantage of. This does NOT however, mean that nair is a bad approach option. Contrarily, it can be a really good way to cut off space and approach an opponent not necessarily going for a hit.
The hitbox of nair, shown above, does not cover directly below marth, and it's obvious when you look at it. Moves like dtilt are much better for grounded approaches, and there's not question about that. So why do marth's use nair a lot, and so unsafely? It's not impossible to use correctly, so there's definitely some misunderstanding here.
Let's look at the Marth/Fox matchup for an example. You are correct when you said that Mang0 could get the shine under PPMD if he threw out the nair. But that's because PPMD(at least in the example) threw out the nair at the wrong situation. Foxes can easily maneuver under nair's hitbox and shine, and here is an example that isn't the one you are describing
https://youtu.be/OC_mcXzGZbE?t=1m40s
Arc did a nair after getting his shield baired. The reason this was the incorrect decision was because not only did the back of the hitbox completely miss Lucky, but he was also able to run under him and regain center stage.
So when should Marth's be nairing in the matchup if it's so hard to hit Fox with it?
There are much better posts and discussions about this same topic by much higher level players, but I'll try and put what they said into my words.
I believe that nair is a move that is best used to cut off options for the opponent, as an extension of your dash dance. The one place that nair finds the most success is in the corner. The reason for this is because when Marth threatens Fox's limited space in the corner with his dashes, most Foxes would want to jump, to the platform and away from Marth's grab/dtilt, and that essentially covers it. When used in other positions, it's used as more of a way to control space, but because of how unfavorable it's hitbox is, I wouldn't really recommend it there, unless you were sure that Fox wouldn't be trying to move in, and thus establishing respect for the move (which imo is better done in the corner) and if you watch top players, you will find that their play will generally agree with that.
Here is an example of good nair usage:
https://youtu.be/K6E6Zp5sYvs?t=2m13s
Note that Armada doesn't get hit by the nair, and when PP moves in, Armada jumps up the the platform, and full hops over into center stage, and PP reacts to him coming down with fair into fsmash, which wins him the game.
To conclude, nair is a good approach option when spaced properly, and when it can threaten a stationary or limited opponent's space.