JonF, I have no plates or personal experience of Zante. However, if the surface wind is calm it may be simply that 34 is preferred for arrivals (perhaps ILS only on that runway for example/terrain/noise) and 16 is preferred for departures (terrain or noise abatement reasons for example).
EDIT:
In fact, having just checked on google earth, I see that the 34 end is only approximately 775 meters from the shoreline. So, I guess, wind permitting, it makes for less noise and pollution for the locals to land and take-off over the sea.