Well. According to the fact that I drew a Masterball, yes, Legendaries will be made available, as soon as we hit an interesting land mark, ect.
Since they're bound to be popular, yes there will be multiple allowed of each type, and shinies, and if I'm feeling exceptionally interesting, they'll even breed. The primary source of Legendaries will probably be the "woo a hundred pages!" sales, or else things like customs.
...of course I could always end up doodling one in my spare time, and then a masterball will show up randomly in a flatsale, and oh the fervor.