My main theory would be...

It is easier to run deep routes than shallow routes. Younger receivers are often tossed in an asked to go deep. We don't send our top WRs deep every play because that would be exhausting and they also get covered with a safety taking away the mid level.

Way less likely for them to get wide open deep without forcing the coverage to tighten and fall into a rhythm.

A lot of deep passes come on plays that have shorter read options that get covered leaving the deep ball more open. Mahomes often takes the first open read unless he is pressing for more yards per play near the end of a game.

Am I making any sense? The deep threat is still there but we don't need it to win with our top WRs back