1) The signs are usually not complex, you can easily read them yourself when you see them on TV. One finger might mean a fastball, two fingers some kind of breaking ball, three fingers might be the pitcher's least favorite pitch. Often, the sign is accompanied by a second sign indicating where the catcher wants it. So one finger followed by a hand lifting up-up, means he wants a high fastball. The players will know what the signs mean after one batter at most.
2) The only time the batting team can actually see the signs is when there's a runner on second. In this case, frequently, the catcher will go to the mound and he and the pitcher will come up with some simple obfuscation. Normally this looks like 3-4 signs indicated in quick succession. I assume they've agreed that number 3 is the meaningful one or something.
3) The communication doesn't have to be perfect. In a lot of cases, a batter is waiting for a specific pitch. It would be enough to signal "Yeah, it's gonna be a fastball outside".
The article suggests that a specific camera crew was the original source of the signs, but it's not clear how that worked. It happened in Boston, so perhaps the camera was manned by local people who turned out to be red sox fans. If such a person was watching a continuous feed, and a specific redsox player asked to be alerted when a high fastball was coming, the apple watch would seem to be a practical solution.