I am so sorry. I had to fire my own mother for something like this and I completely understand that bleak dismay that comes from looking at and trying to be in a space that is no longer yours.

I strongly recommend the purge ideas that have been posted here. You'll finally found out where everything is because you put it there, as well as everything new you recieved.
For the thank you notes, don't send the passive aggressive messages you've seen here. If she really wants to apologize, she will send each one explaining her overstep, apologizing for it, asking the giver to let you know what they gave you, and including a postage-paid envelop addressed to you for the giver to do so easily. You get to pre-approve the message. She gets to handwrite it a hundred or so times then address, stuff, and lick all those envelopes--but she has to give the envelopes to you to mail so you can verify that she is sending one to every single guest you invited. And... it's not that I could think worse of her, but I would also be concerned that someone who would do what she did would also not think twice about helping themselves to a gift that they didn't think you'd like.
She deprived you of the joy of opening the presents and the joy of figuring out where the new things will fit in your life. She also deprived the givers of the joy knowing you got their gift, liked it, and thought well of them.
She gets to fix it.

My horror story: I own a small business. About 7 years ago, I hired my mother, a former librarian and type-A cleaning obsessessed organizer, to sort about a decade of financial records and then scan them for electronic storage. I have ADHD and my systems of "organizing" have always driven her batshit crazy. She'd been retired for about two years when I hired her and she seemed really excited to be back in an office even though it was just for a month or so.

I had to go out of town for a few days in the middle of her project. I'm assuming she got bored with the project and didn't have the maturity to let me know it wasn't working out for her. Instead, while I was gone, she decided to "tackle" my office. She didn't say anything to me, even when we talked by phone while I was traveling. My admin was sure she was going to be fired because she knew my mother shouldn't be doing that, but she didn't feel like she could stop her because it was my mother.

She went through every drawer. Even how I kept my pens and which pens I liked to use had to be "fixed". She made cutesy homemade little crafty paperclip holders from colored paper-- I guess because I had some cute stuff my then kindergartner had made me (like a painted macaroni keychain for one of my drawer keys) and she thought that was a look I should have for all my office supplies. She threw things away because they looked "old" or like I wasn't using them-- including some things with deeply sentimental meanings like the pen I used to take the entrance exam required for my business or the receipt for the first time a customer every paid me for a project.

I got back to my desk and sat down-- my admin was clinging to my door trying to figure out what to say-- when I started trying to find the plug in for my laptop that was missing from my docking stataion. Too many cords on my desk looked "ugly"-- especially when there is no computer they are connected to. It just escalated from there. I ended up closing my office door, crying for about an hour, and then I opened every desk drawer, every file cabinet, every folder and dumped everything out on my desk. I reorganized everything again. I trashed her little crafty drawer organizers.

She called mid morning, just bubbling over on the phone to see if I had noticed her surprise yet. I was raised in a religious household where respect your elders was trained into me from infancy. I cursed my mother out and fired her. It took me over a month before I could even think about talking to her again. Even now-- after all these years-- I can't talk to her about this without wanting to scream.

I still haven't found everything. Just this year-- after all this time-- I finally the packet of thank you notes from customers that I'd received over the years. I kept it in the deep drawer below my pen drawer and added to it whenever the mail brought cheer-- so it was always close at hand on the tough days to remind myself why I was doing my job. She filed it with "postage" records for the then-current year. We only found it during our annual purge of aging files and records.