I took notes in LaTeX for all four years of college, including upper-level math and CS courses. It worked fine for me. Once you get used to it, typing most symbols is just as quick as writing them. Long formulas or lots of embedded fractions and things make it more difficult, but you can still type it pretty quickly, especially if you don't worry about compiling it as you go (which I did, and which was perhaps a bad idea since it does slow you down).

As some other people here have suggested, you can also define new commands to help you. One class I was in started using a lot of diagonal matrices, so after being slowed down a bit the first time I defined a new command that would easily let we write diagonal matrices. You can similarly define new keywords or languages or whatever you need to help you stay on top of things.

It might not work for everyone, but if you type fast and know LaTeX well it is easy and can work well.