Had this happen once at 11U, twice at 12U, once at 13, and once so far at 14U. The last one was a hard shot up the middle that one hopped to the CF traveling to her left (glove side). The CF threw a perfect strike to first on the run to save a no-hitter. Heads up play, but it's never practiced or encouraged.
In all 5 cases, the runner was out at 1B. Saw it attempted 2 other times where the throw was on target, but the runner beat out the throw.
Like I said, this isn't something that kids are instructed to do, but certain players with a developed situational awareness will pull this one off on their own. I don't see any good reason to discourage them from thinking on their own and testing their abilities. It's their game to play...allow them to take ownership of it. Of course, if it totally blows up on them and hurts the team, it's on them as well. Risk vs. Reward.
At the HS level, I see lots of the opposite problem. Marginal outfielders who loaf to a fly ball, only to hold up and keep it in front of them...at times with empty bases.
Of these two scenarios, which one is easier to "fix?"
I actually saw this attempted once by a left-fielder in the Spano Dome at 12U from a guest player from a well-known high-level team. Good throw, but late by about half a step.
Luckily, none of these occurred in a tight game which would have affected the outcome either way. Play loose and play confident.
I'm sure that a runner thrown out from RF looks odd or bush league to most fans of baseball as well. Though it's not that uncommon in softball.