I've not removed manifolds from my FJ, but have removed from a couple of 200,000 mile V6 Camrys over the years. In each case the fasteners at the manifolds were all fine, because they get so hot during use that no moisture was able to start them rusting (also because being cast iron the manifolds themselves are naturally resistant to rust, compared with carbon steel pipes).
If you do break a stud there are about 50 options for how to get the stub out, each depending on access and how much is left sticking out. In general, the fastest and most risk free method is to weld a nut to the end and use that to turn it out.
It's a tight fit but they are not hard to remove. I recommend having long flex head ratcheting wrenches and swivel sockets on hand before attempting it. Also soak the nuts/studs a few times with PB blaster before attempting to remove them. The studs can be easily removed with a regular stud puller. Do not re-use the gaskets, and stick with the OEM gaskets rather than aftermarket. Like Norm said there's a bunch of ways to remove a broken stud but this is best to be attempted by a professional.