First off, the shadowcaster uses "mysteries", not spells. This may occasionally be important somehow.
Fiddly bits aside, to answer your first question, if the shadowcaster's higher level mysteries became supernatural abilities, the class write up would say so. It doesn't; as for why, you'd have to ask the designer- IIRC the shadowcaster was designed by [MENTION=1288]Mouseferatu[/MENTION], but I could be wrong.
As for the feat, it's pretty plain- you do NOT gain any additional uses of the mystery in question unless you already have the ability to cast it as a supernatural ability. If you have that ability or later gain it- in other words, if it's an apprentice mystery and you are 13th level (or become 13th level) or higher, or if you've already invested in feats to make it a supernatural ability- you gain an additional ONE use per day. It doesn't matter how many times you take the feat; it always gives you ONE extra use each time you take it for such a mystery.
So let's say you are above 13th level and taking Favored Mystery (prison of night) twice. It's normally cast as a spell, since it's a master mystery. Take FM (PoN) once, and you can cast it as a (Sp) ability; take it twice and it becomes a (Su) ability, usable an extra 2 times per day. (And since a Su mystery is normally usable 3/day- see ToM pg 138- you're right that it becomes usable 5/day.)
So yeah, you've got part 2 right.
As for epic mysteries or new paths, the stuff in ToM is some of the only stuff in my 3e collection I never expanded on. Sorry- I think it was just too late in the edition's life cycle for me to get to it.