I read once that several villages in Europe whose population had been wiped out by the Black Death were rediscovered in WWII due to air recon photos. Were these villages ever excavated or examined?

I can't speak for the whole of Europe but can offer a British (or perhaps only English) perspective. Indeed many villages were hit hard by the Plague over time, some even disappeared completely. Nowadays these are known as Deserted Medieval Villages or Shrunken Medieval Villages. Excavations etc have been limited, mostly due to the fact that there is comparatively little to learn from them for a few reasons. 1) they are basically the same as modern villages, their size and layout have changed very little. In most cases the important buildings have survived in one way or another, be they the parish church or the manor. The archaeological evidence buried in DMVs is the same, more or less, as found in current surviving villages. For every DMV there are (I would estimate) 50 surviving villages. 2) two DMVs next to each other will be almost identical archaeologically speaking. Relatively little can be gained by excavating both compared to just one. 3) a lot of villages which are now a lot smaller than they once we're are so because of more recent trends. C20 population shifts due to agricultural mechanisation and industrialisation have seen village populations fall by a lot. It's only in the art few decades have they recovered their population.

With regards the air surveys, it is true that a lot has been seen through aerial observation. However it is perhaps misleading to say that they have been rediscovered. Most places, even when they lost almost all their population were still known about, and indeed they retained their name and location in the local and official record. So whilst it has been extremely valuable to see crop marks etc showing their former extent, to say they have been lost and rediscovered is not really true.