The Help thread is a better place than this, especially as some of your questions deals with XD...well, one, but still. Help thread.Um, can you like, in this game, get more than one of the same johto starter?! Like, get three chikoritas, three cyndaquils, and three totodiles? Can that be done? Also, can you battle the cipher admins with the legendary dogs over and over, and re-capture them over and over even if you caught them already? Can anyone understand what I'm saying? Can you do this?
But anyways - no; you can only get one of each of the Johto starters max. Of course, if you start a new game file you can get another set.
And for the second answer - again, no - there is only one of each Shadow Pokemon - you cannot get more and more legendary dogs or any other one - just the one of each 48 Shadow Pokemon. Again, if you do want more, start a new game file after trading the ones you want onto your GBA game.
(But you can still rebattle the admins even after you've caught the dogs; but there's nothing to get out of it besides experiance for your Pokemon, and the chance to hear Miror B's salsa music once more).