I cannot answer all of your questions. But from my experience brake failure is extremely rare. It does affect all normal brakes and the station brakes. However, it does not affect block brakes, even in continuous operating mode. So when I create a coaster that will run without block brake mode, I always add two block brakes back to back before the station. After building a block brake you have to remember to change the coaster back to continuous mode since the game will default the ride to block section mode whenever you build a block brake. But two block brake track pieces is enough to slow the trains to a safe speed in the event of a brake failure. For some reason just once block track piece doesn't always work. I've noticed inconsistencies with the speed at which just one block track slows the train. Anyway, that's my method to ensure no crashes.
As for your crash you cannot figure out, sometimes a safety cut out will stop the lift chain and the trains will back up at a lifthill. Then when it restarts, if there are some trains full and some empty, the full cars can catch up to the empty ones, sometimes at speed, causing a crash. I've had a mine car ride that would crash randomly after breakdowns. Always fun to troubleshoot and then try and build a safer coaster. Hope this helps.
This video may also help for derails...this guy does very informative videos on all sorts of RCT2 stuff:
https://www.youtube.com/watch?v=P5l0Wl8xD2k