If combat is infrequent, how do you fill in the gaps? With riddles? Exploration? Good topic, I'm interested in it myself.
You don't have to fill the gaps.
When I think of this, the two main games which come to mind are Thief and Deus Ex. In these games which are of course not roguelike, combat is often an option. You can play the game and choose to make combat as infrequent as you can, pick locks, walk in the shadows, activate a speed augmentation/implant thing, enter a giant weirdly man-sized air conditioning system etc. And so it isn't so much that a gap is a gap, but rather that the gap is an exciting event where the attempt to avoid the potential combat is content in and of itself. This can be factored into game design, procedural generation and the rest.