So its not a surefire way to beat the ninja bosses before they get to your gems, but it works about 1/4 of the time.
Frozen ninja's can't go invisible, so in the undead talent tree when maxed out crypts have a 25% chance to freeze targets, so if the first tower you have hit the ninja boss is a crypt there's a decent chance he'll get frozen on the spot before he can go invisible, allowing your towers to blast him to death.
If you start a level and leave it on the "level goal" screen, drowning tourists will spawn but their timers wont go down, so you can wait a bit and start the level with extra cash from saving a bunch right off the hop
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 "Vacation Mogul"){kind=icon}