I guess it all comes down to sound design, loud things like percussion should be in the pit, but in a show like Lion King those instruments are too big for the pit and it can be distracting espicially if you are sitting next to that particular box. It isnt so bad at the Minskoff since those boxes are high up, but in Toronto I sat next to the box and it was very loud and distracting.
But if you want a bigger orchestra, it is not always possible to enlarge the pit (some shows have sub stage scenery right behind the pit)
At the same time, most of the time box seats to suck so it is nice that they are being used for something else. I noticed in London that Phantom has a Piano in one of the lower boxes, but that's just for rehearsals.
http://www.flickr.com/photos/27199361@N08/ Phantom at the Royal Empire Theatre