Take the high road. Always. That means being a welcoming hostess and not keeping track of how many people came and what they ate. Don't judge other people for their economic situation - maybe all they could afford was a small toy and a recycled bag. Teach your son to be grateful for every little gift he gets, and not to treat a birthday, as some people do, as an opportunity to haul in a bunch of gifts with gift receipts so they can be traded in later for something really good. Parties are just that - celebrations of the birthday or other occasion. Gifts are nice for guests to bring, but they are not the admission fee for someone's attendance. So you did the right thing by sending a gracious thank you, and not implying that there was anything deficient in her gift. That's where you should have stopped.
So she asked to have her family members come - a little tacky but maybe they were visiting and she didn't want to choose between them and you, maybe she was a little uncomfortable and wanted familiar people with her since you would be busy with party stuff. Maybe she's just rude. It doesn't matter. You said "yes" and you don't get to exact payback, as if you were saying to her, "Well, okay, they can come, but I'm keeping track and you own me."
She had a party and didn't invite your two-year-old son? As other's have said, maybe it was a princess or fairy party and she thought it would be beyond him. I'm not into gender-specific parties, but some people are.
But you don't know the specifics. Maybe she just can't handle a big crowd and she's already got family who show up for everything.
Some of the other families were invited, but maybe not all. You don't know but you're already offended.
So you take the high road, as I said. Repeat that 10 times a day to yourself. No, you do NOT say that you know about the party. You don't send an email about something else and include a note about the party. I wouldn't send a gift - this mom probably already feels uncomfortable about not having everyone, so you don't rub it in by sending a gift. Again, if she has financial constraints, it may make her feel worse knowing that you have enough money to send gifts to everyone. Again, the children are TWO. There will be many, many parties in these children's futures, and not everyone will go to everything. Saying you know about the party is purely passive aggressive, or it will be seen that way. Don't give yourself a reputation for being ungrateful or someone who sticks the knife in and twists it. You don't respond to an insult (real or perceived) with another one.
You concentrate on teaching your son to see the positives in life and not to get miffed about every perceived slight.
Just respond to the mom's email and stick to that subject alone. That's all, nothing else. Show her that you are a mature person who doesn't judge her worth by how many two-year-old parties you get invited to.
The more classy a person you are, the more classy people you will attract.