yes,u can encounter cards that u already have in your character decks,the only restriction is that,If you aquire,and they are more than u have in your vault,the surplus copies are deleted at the next scenario startup:
example, u have 2 copies of 'Noble brat' in vault, and there are one in Valeros deck and one in Merisiel deck; during a game,you encounter other 2 noble brats...if you acquire them and then add to merisiel and valeros decks(So u have 4 of them,2 per deck),when u star a new quest with Valeros and meri,u have to discard two of them,before playing(a menu appears and allows u to make this);If you add the two extra noble brats to other two characters,if in a game there are just 2 of them,u can use them without previously discard them;so,example,if u encounter two noble brats and add them to Ezren and Kyra,and they don't make a group with Val and Meri,there's no problem('cause,in game,just 2 cards are used in decks). the secret is to manage the groups in the correct way,knowing how many cards u have in the vault....especially for blue,purple or golden cards