I have found a lot times an ufo lands over non populated areas for Harvest Missions; no civilians were present in the map, so I wonder what are the aliens harvesting :P

There are 2 issues with this, the available spawn points for civilians in some mapdefs (even for nopopulation a mapdef should be able to host 2 civilians), and the way a location is chosen for a harvest mission.

Checking /src/client/cgme/campaign/missions/cp_mission_harvest.cpp found CP_HarvestMissionGo() as the responsible to chose a location:
# Chose a mapdef.
# Check if some nations should be favored (due to XVI).
# Get random position on Geoscape, counting favored nations if needed and mapdef chosen.

I know there is a todo note:
@todo Remove me when CP_XVIMissionGo will be implemented

I also take into account the difference between Harvest and Terror missions, but I think it could be easy to improve the way a location is chosen to ensure a minimal population will be present (suggested code in the attached patch). Another matter will be if the mapdef contains or not enough spawn points for civilians.
# Check if some nations should be favored (due to XVI).
# Set a list of suitable population values; "urban", "suburban", "village", "rural" (avoid just "nopopulation", so the only current mapdefs excluded would be "+ice" and "wilderness").
# Get random position on Geoscape, counting favored nations if needed and a linkedList_t of suitable populationTypes.
# Chose a mapdef suitable for that Geoscape position, populationType and UfoType.