the short answer is yes, you will get BP for killing the troops and you will fight at 100% morale.
i like to think of it like this... you get BP for farm space of units you kill, the units in the farm villages don't take up any farm space (since the villages can't hold any population) so you get no BP for killing them. the units in ghosts however are using up farm space in the ghost's farm, and used farm space when the (ex) player built them, so you get BP for those.
as for the morale thing, morale is a player vs player thing so you need to take the total points of a player you're attacking into account. so i guess casper/ghost is the biggest player in most worlds

either that or ghosts just aren't a player so you aren't penalised for attacking them
