A few things I've noticed on my WPC games:

If the game has physical ball locks, and a game ends with 1 or more balls in the locks (and not in the trough), and the player quickly starts a new game before the game can kick them out to drain, the game will begin a new game just fine (without a ball search or "PINBALL MISSING" display. When the game is played, it adjusts the game rules to account for the locked balls (i.e. if you lock a ball for the first time, It'll kick it back out from the lock and not the trough, as if you were playing a multiplayer game where someone already locked those balls). Not sure if that was relevant to anything that you're doing, but it's definitely worth mentioning if you haven't ever noticed it before.

To answer your question about a ball drain, and what detects a lost ball, it's a two step situation I've observed. On my White Water, if a ball drains into the outhole, but it is NOT kicked into the trough, the game will begin the end of ball jingle, but quickly realize that it hasn't been kicked into the trough. It'll then snap back to "main game play" but also cycle a ball search. In order for the game to properly end a ball, the ball needs to drain into the outhole, get kicked into the trough, and depending on what balls are locked on the playfield, activate one of the ball trough switches.