Bonsai Humidity trays are important for healthy Bonsai Trees for the following reasons:
1 - Since all bonsai pots have holes in the bottom for drainage, the humidity tray will protect the surface of whatever you are putting the tree on (windowsill, table, etc.)
2 - You should always leave water in the tray so that as the water in the tray evaporates, it will create a constantly humid environment for the tree and help offset the loss of transpiration (the loss of moisture through the leaves.)
This will not provide necessary water to the tree's roots in this manner therefore you must adhere to the tree's watering schedule by watering down from the top of the soil.
3 - Instead of taking the tree to the sink to water it, you can simply water the tree in place. When watering with a glass or watering can, pour water on top of the decorative pebbles slowly until it penetrates the soil and the excess water comes out of the holes in the bottom of the pot. Then fill up the rest of the tray with water. This method is particularly convenient for watering larger trees.