So I just filled in a layer in the ceiling of my skeleton spawner as it was bugging me that there was only one layer of dirt between my base and the dungeon. Then it seemed like I was getting reduced spawns from the spawner, the skellies only spawned either solo or duo with the rare exception getting a tri-spawn. I've yet to see a quad spawn since I filled in a layer above the spawner block, which was a pretty common case earlier.
Therefore, I'm wondering whether I've filled in a bit to much. As of now, There is only one layer of air above the spawner block itself; will this affect spawns in any way, shape or form? Does it have to be two layers of air above the spawner in a 8x8 area in order to up the spawning quantity?
Yes, only one layer of air above the spawner is not sufficient. It is a possible spawning area, but any mob 2 blocks high will not spawn as their heads will be in solid blocks. Make your roof 1 higher or you are limiting your spawns by 1/3.
Mobs can spawn with their feet in the same level as the spawner itself, or one block above the spawner, or one block below. For 2-tall mobs like zombies and skeletons, this means their head will be two blocks above the spawner, if they spawn in the top-most possible space. If this layer two blocks above the spawner is filled in, though, then no mobs will be able to spawn there, because they can't fit. Limiting the available spawning spaces in this way will almost definitely affect the rates you will see in your trap.