[Time2Ref]

I don't think that the coaches are telling the players to do this. On the other hand, I don't think the coaches are telling the players NOT to do it.

If it bothers you, just mention it to the captains in the pre-game. Then, if it happens in the game, you can stop it as soon as you see one of the players moving towards the free-thrower.

I don't think the players even want to do this anyway. It started as a congratulations for a sucessful free-throw. That seemed to put extra pressure on someone who misses the first shot by "its absence". Now, they think they need to do it after every shot.

So, to answer your question: Don't warn or penalize it. Just let them know you aren't going to allow it.

As rainmaker pointed out, it's not a big deal unless it is delaying the game.

Plus, as you mentioned in the OP (4-47-2 & 10-1-5), the NFHS doesn't want this happening.