An empty Estate only collects half taxes yes.
I'm a bit confused to what Foundation said, but if I understand it right with Penchant's comment, it still is affected by its efficiency. So a 90% vacant estate would collect 100 * 0.9 (efficiency) * 0.5 (vacancy) = 45 gold, while wildlands would generate 50 gold for the Lord. Is that right? If so, wildlands would generally be more efficient than vacant estates, and never worse. Perhaps vacant Estates should be treated as wildlands, as I erroneously believed was the case.
