So the people who run the event don't actually do anything with all the manuscripts they receive?
They don't receive any manuscripts (except perhaps erroneously from a few participants who mistakenly thought otherwise). There's a place on the website where you can paste your novel and it will count the words in the MS (it may not even send it to the server - it may be a bit of Java running on your browser that counts the words), to update your wordcount on the site, and verify when you actually pass 50,000 words and become a "winner." With thousands of winners, there's no way they could read even a small fraction of them anyway.
One agent posted, "Don't send us your NaNoWriMo entries."
I felt kinda bad about it cuz it really wasn't a very raw MS.
That's because of another (regrettably for the agents, not too small) group of NaNoWriMo participants who don't read the directions, and think the first draft of what they just wrote is publishable. That's basically what they mean, "don't send us your raw MS."
If you've edited your MS and had it read and critiqued by beta readers who think it's as good as a "real" novel and ready to go, bla bla bla, then go ahead and query, and send as requested. It might be good not to mention the words NaNoWriMo or the month November, as that might unfairly bias an agent against your MS.
Once it's sold to a publisher, feel free to brag about it being a NaNoWriMo novel - they've got a page somewhere with the names of published novels written for NaNoWriMo.