I like cut in windows on some of my bows. I like locator grips a lot, and even w/o a cut in shelf, I often have a bevelled leather tab, hemp binding, or whatever for a partial arrow rest.
The only real issue is that you have to respect the wood for what it is. I have seen so many guys over the years try to make essentially all- wood copies of FG bows, and it just doesn't work well that way. Like Dean Torges said, the ability to, say, slightly crown out your fadeouts on the belly allows you to make that transition better and more gently than a FG bowyer ever could. BUT. You often also NEED all the limb length you can get on a wood bow, and a massive riser with a huge cut out shelf costs you that.
DOING it is fairly easy. Make sure you have that little extra thickness in the handle, and that the bow has all the mass in both thickness and width it needs right at the fades. I put the grip where I always put it; the base of my thumb in the physical middle of the bow, mark below my pinky, and three fingers above my index finger. Fades extend maybe 2" above and below that, crowd the transitions a little, and the whole thing can be about 10-11" long. Usually I make these bows with more symmetrical limb length.
Then just don't get too aggressive about how tall or deep the cutout is. I cut well in, but don't see the need to force the bow to be centershot.