The answer is implicit in the section of the spellcasting rules on areas of effect (Player's Handbook, Chapter 10):
A spell's effect expands in straight lines from the point of origin. If no unblocked straight line extends from the point of origin to a location within the area of effect, that location isn't included in the spell's area. To block one of these imaginary lines, an obstruction must provide total cover, as explained in chapter 9.
Obstructions that provide total cover, such as dungeon walls or floors, therefore limit the area of effect. This would mean that in your example, the cylinder goes from floor to ceiling, but not above, as the ceiling provides total cover to anything above it excluding the presence of holes.
As Anaximander's comment (below) puts it, you can think of the Area of Effect as light originating from the point of origin. If a target inside the Area is fully shadowed, it has total cover and is not affected, unless the effect is stated to spread across corners.