They are a kludge to force the plane to fly a departure as it is supposed to. Leaving them in will never cause a problem unless you miss one. The AP wants to fly through each point in order. If you takeoff and miss one, by not flying close enough to it, it will get confused and may turn around to try to get to it.
If you make some kind of mistake on takeoff and can’t hit one of those, you have to be smart and not just turn the AP on and expect it to read your mind. You use the DIRECT TO function to make the plane go to the waypoint ahead of you and skip the one you missed.
I’ve never had this problem with the AP because I actively manage it.
But telling people to “just delete them” will make the plane not fly the SID or STAR correctly. And in some cases it will make the plane do crazy things