An article from the UK Times Online tells about renovators finding bee hives built in to the architecture of the Scottish Rosslyn Chapel.  They were located near the roof when the church was first built.  The reason for attracting bees there, however, remains a mystery.From the article:

Allan Gilmour, from Hunter & Clark stonemasons, the main contractors on the chapel, said: ?I?ve never heard of man-made stone beehives. …?Maybe at Rosslyn the monks had the same problem in the past and created the hive as a sanctuary.?There is anecdotal evidence that visitors to the chapel, which dates back to 1446, used to be disturbed by bees. Mr Mitchell said some of the staff at the Rosslyn Trust were aware some years ago that there had been bees going into the cavity. The hives have now been reinstated within the rebuilt pinnacles on the roof of the chapel.

Interesting.  Reasons for the hives?  As the story suggests, perhaps to draw the bees away from burrowing in other areas of the church where they would be more of a nuisance to worshipers.  The only other reason I could think of offhand is if they were desired to cross-pollinate nearby orchards, but I doubt that farmers of the 15th century would have known about the role bees play in that process.