Well, yeah, they can read to break, but it is much harder from what I've seen. Essentially, meaning more players will guess the mix up (like the close to ambiguous crossups in games). From what I heard from some pros playing KI, the combos with manuals are much stricter, but the payoff is less of a breaking chance.
If you can do 1 frame links in SF, I couldn't imagine manuals would be much harder. The auto double is pretty much a dial a combo.
i'm not sure what you mean by reading. well i mean i do, but i guess it depends on if the person is using the same manual over and over or mixing things up.
for instance, jago's one double roundhouse manual is very easy to see and break on reaction. however the timing for it is much tougher than trying to break his heavy auto double, which is also very easy to break on reaction. i think you have 1/2 the frames to break a manual if i'm not mistaken.
as far as manuals being "hard" to pull off, i mean they are hard to pull off in the sense that you will get auto-doubles a lot when you don't want to, and with jago's roundhouse kick, it's easy to break a botched double roundhouse kick because it will be a heavy auto double. but that is just an example, i know there are also medium and light manuals. like jago has a mp linker, that is only 1 hit. the fact that it's 1 hit makes it much tougher to break as well since all auto doubles (except shadows) are 2 hits.
it's going to get tricky when people start mixing auto doubles in with manuals though. i'm no where near that level yet. i'm still at the point that i get flustered and in my head i know what to do, but i can't interpret it into the game 1/2 the time because there is simply so much stuff going on at once in this game that i get flustered. i've never played a fighter where there is so much going on at once as there is in this game.