I haven't had had a chance to read every single comment, but I didi read where you said that the aggression incident occurred as your son was trying to get her out of her kennel. This is an incredibly dangerous thing to do with a dog you don't know well. A dog's kennel needs to be a sanctuary where they can go to get away from other dogs and people when they are feeling overwhelmed/threatened. Since the dog was in a new stressful environment she was doing what was natural by going to her den where she knew she would be safe. This overall is a good thing and exactly what you want her to do when she needs space or feels threatened.
Kennels/Crates can be an excellent tool for helping anxious dogs adjust to new situations. But, there must be very strict ground rules on how the crate is used. The crate belongs to the dog and only the dog. Children need to be taught that when the dog goes to it's crate that it is the dogs way of saying "I need space/leave me alone." Children should never be allowed to play in or around the crate. Although your son was not playing, he was invading her sanctuary, and she was obviously feeling anxious/fearful at the time and needed some space.
In the future, I would suggest that you use treats to lure her out of the crate (and a few feet away from it) before trying to get her to do something. If she refuses to leave the crate, leave her be. She is still adjusting to a new environment, and it sounds like her time at the shelter was a bit chaotic and left her feeling insecure and unable to protect herself.
That being said, there is nothing you have said that suggests that she is an aggressive dog. Just an insecure pup in a new environment. At her age it probably won't take long for her to figure out that in your home she will not be picked on by other dogs/people or need to compete for food, and will probably relax and settle in very quickly.
In the pictures you posted, she definitely looks beaglish (especially the profile shot). She could also be a larger hound breed (harrier/walker) since she does look pretty big for her age to be a beagle. In the pics she also appears to be very relaxed and comfortable with your son. We've had a variety of rescued hounds as pets and fosters (from beagle all the way up to walker coon hounds) and they tend to be very sweet and loyal dogs.