Probably because of the confusing UI in KiCad. It’s just not obvious when a pin or wire is connected or not. Until one has learned the nuances of KiCad, newbies play the safe option.
I’ve been using KiCad for years and it still trips me up occasionally.
You are right. Brief look look at the schematic above and i would say that no junctions are needed there except on 2 wires connecting GND pins 1 and 2 and on SMA connectors.
Because deleting a wire segment at a Tee junction does not automatically remove the now unnecessary junction. I hope the upcoming Eeschema rewrite will address this bug