I've been to Baltimore Comic Con every year since 2010 (except in 2016), I've been to Awesome Con in 2014 and 2016, and I went to FAN EXPO Canada in Toronto back in 2015.
The short answer to your question is: No. There is no major Brony presence at these conventions. If you show up in full Brony gear, you will stand out, but most people there won't really care.
The great thing about MFCs, is that they really are for anyone, and everyone. If you're someone who doesn't like Superheroes, no problem. There's plenty of other options for you, whether it be Star Wars, Game of Thrones, anime, Star Trek, Pokémon, or, yes, MLP:FiM. Although MLP is not a huge feature, you may be able to find pony related merch at these conventions. You just gotta look for it.
Another great thing about MFCs is if anyone form the show attends, it's a LOT easier to get their autograph, then at a pony con. I met Tara Strong at the FAN EXPO Canada, and I only had to wait about 20 minutes.
I'd definitely recommend Awesome Con in Washington D.C., but I only go if there's someone attending that I'd really like to meet. So far, I have met Phil LaMarr, Billy West, and Maurice LaMarche (4 years before he would become Prof. Neighsay) at Awesome Con, and all three were absolutely delightful, with very small lines to wait in.
I would also recommend Baltimore Comic Con. It's a lot more basic, they mainly just focus on the Comic Book Industry, with a lot of comic book writers and artists, instead of TV and Movie stars, but it's cheaper, less crowded, and really gives you an idea of what to expect from a MFC. Also, I don't know if this will interest you at all, but Katie Cook, Andy Price, and Thom Zahler, from MLP:FiM comics are going to be at Baltimore Comic Con this year.