The substructure of the universe regresses infinitely towards
smaller and smaller components. Behind atoms we find electrons,
and behind electrons quarks. Each layer unraveled reveals new
secrets, but also new mysteries.
-- Academician Prokhor Zakharov,
"For I Have Tasted The Fruit"
from the Alpha Centauri game
Therefore, I hold that the gaps are not getting smaller - quite the contrary. It is maybe possible to compare this to an ink blot - the more space it occupies, the longer its boundary is bound to be (OK, I know it depends on the shape, but that's a very different can of worms). In other words, there's always more new whys than questions answered.
Disclaimer: I'm not making any statements about the (non)existence, or even the possibility of such, of God or any other entity in the gaps.