Banksy most likely doesn't care about them being vandalised, he still gets to make his point and picks up the publicity beforehand. The interesting part is that by tagging over them others could actually be hurting new york, Banksy pieces have been known to attract visitors (as with the one in east new york) and may even increase property values (though never proven).
On the other hand, the residents may just appreciate the artwork and not consider it to be vandalism, but some guy scribbling over it because "this is his turf" is. Usually pieces tend to remain intact for quite a bit longer but ny vandals seem to have taken a dislike to him. If they actually responded with art (King Robbo[0] as an example) I'd call fair game, but scribbling a quick tag is just vandalism.
[0] http://twistedsifter.com/2012/01/banksy-vs-robbo-war-in-pict...