1. "How much do you weigh?" <- This sounds most natural to a native English speaker.
2. "How many kilos do you weigh?" <- You might hear this from a native English speaker in a country using metric measurements. It's less common than "How much do you weigh?"
3. "How much is your weight?" <- This is grammatically correct, but it sounds unnatural to a native English speaker.
"How much" is used with nouns that are uncountable.
"How many" is used with nouns that countable. (In #2, the countable noun is "kilos")