How to use and is there a good thermometer for very small small fish?
Whitebaits are thin. If you are putting them into hot water or hot oil, it should take under a minute for the whole fish to reach the temperature of the surrounding liquid, assuming they are no thicker than 5mm. Heat transfer at this scale is rapid. If you have frozen whitebaits of course, that would take much more time. My suggestion is to cook them once thawed.

It is not practical to probe the inside temperature of such small fish. Your thermometer, unless faulty, should be well capable of measuring the temperature of your cooking water. You would have to design an elaborate experiment to get at the core temperature of the cooked fish. Unless you are after the data rather than wanting the fish cooked, don't bother.