They were probably supposed to get you to bonus levels, yes. Probably from 100, as it stops counting after 100. Although in Rabbit in Training, it says (to the order of) Collect 100 gems to get an extra life. In Treasure Hunt, of course, they let you win if you have enough. In Single Player, coins turn to gems once you've gone through a coin warp, so this is one more (albeit useless) use of them.