16 weeks old is still a baby. She is still in her socialization learning phase and normally, mama cat and siblings would still be in the picture helping to teach her how to be a 'cat'. What she is doing when she hears a loud noise is a fear response - not anger or moodiness. She is afraid and she growls because she doesn't know what else to do - she is trying to protect herself. I suspect she was very young when she left her mother and still feels very insecure.
Cats do NOT respond to training by punishment. What is actually happening when you flick her ear or forcibly hold her and use a loud voice is to frighten and hurt her. She doesn't make the connection between her activity and the punishment, so now she is also frightened by those who also nurture her. She is not angry - she is frightened and very confused and responding the only way she knows how - by hiding or trying to protect herself.
Kittens at 16 weeks are playful and active. They do get into mischief - not because they are bad - but because they are still learning how to hunt and climb and do all of those normal 'cat' things. When she starts doing something you don't want her to do, don't punish her - 'redirect' her attention to another activity. Interrupt her by gently picking her up and taking her a few feet away and playing with her, or giving her one of her toys, or even just holding and cuddling her. Don't forcibly hold her either but that will only make her fight to get away. If she goes under the bed, try to get her out by playing with her - dangling a piece of rope (not wool or thread or string) or a thin belt and luring her out into play. Instead of punishing inappropriate behaviour, try rewarding good behaviour instead so your focus is a positive rather than a negative one.
And give her time to learn what is acceptable and what is not. It won't happen over night -afterall, she is still a baby - and I am afraid that if you continue the way you are, you are going to turn her into a frightened, anti-social cat who will eventually become aggressive as a means to protect herself.
There are some good books available at pet stores on understanding a cat's personality and how to 'influence' their behaviour. You might want to buy one and have everyone in the family read it.