I don't think it's as conspiratorial as a master agenda from the WTF. I've had punches not score that I thought should have, but everybody I know who has said that also says it about kicks---I've had lots of those not score when they should have too. Now that I've sat as a corner judge some and seen how tough the job is, I agree with what my master teaches: you have to do 3 things to score--1) hit with shocking power and on-target; 2) be in a position and angle in the ring that at least 2 judges have a clear view of the strike; and 3) sell the point (carry self with confidence, kiap, celebrate the point, have hit earlier with power so judges give you any benefit of the doubt [judges are human]). Kicks hit harder than punches and are harder to get on target, both of which are good reasons to give more credence to kicking than punching.
Lots of kicks don't score when they should either, and leg movement is easier to see than arm movement--because arms are easier to hide behind the trunk. Having judged a little, good judges don't score based on sound or guess; they score what they see as a clean point.
I do think legitimate punches are scoring more now than in the past, so I think the balance is improving for scoring of good punches. However, I don't want punches to score easily. If they did, then you'd see more of the garbage we see occasionally at open tournaments: a (usually chunky 30+ yr old) guy (seems like always with a beard) will show up and wear TKD gear except you'll see him strap on his MMA or bag gloves. When the match starts he throws a low-n-slow front kick as an entry and then bulls forward throwing punches until he shoves you out of the ring or you cut around him and kick him. I loved fighting those guys as a colored belt, but it's ugly and lacks skill except as movement practice. There's a reason you don't see that in black belt rings.
Carl