Broodhatch Nantuko states "Whenever Broodhatch Nantuko is dealt damage, you may put that many 1/1 green Insect creature tokens into play". However much damage is dealt to the Broodhatch Nantuko is the number of 1/1 tokens you can put onto the field.
So, if you block a 3/3 with Broodhatch Nantuko and the damage hits without being prevented, you will indeed get 3 1/1 tokens.