I would say if you are seriously pursuing playing in college you better not have a problem with your stats being published.
Others have already stated the stats are only as good as the person entering them so, it is the coaches responsibility to insure the statistician understands the role and what the expectations are. If handled correctly it can be a very good measurement tool for coaches. I have been blessed to have two very good people over the past 10 years handle this.
Good programs can also help a coach in many more ways than just offensive stats.
Like Must stated, Most varsity High School teams post team and individual stats as will the colleges so, at 15 and up is is information that will be public on profiles etc.
Under 14 keep it to the individual but make it available to them. The program I use allows me to pick and choose who I want to have access to what so, the numbers can be viewed by coaches, individual parents or public.