ldolse - The duplicate-checking only works with the same dictionary, yes; the headword and pronunciation aren't even included in 1.0-format flashcard databases, so checking for duplicate words would require us to go through every single card already in the database, retrieve its headword / pronunciation from the associated dictionary and check it against that of the newly-added card. So as you say in your second post, if an import card gets linked to a different dictionary than the card that's already there it won't be marked as a duplicate.
In 2.0, though, headword information is stored in the database along with the dictionary reference (as evidenced by the "headword" and "pron" search options in Manage Flashcards), so it'll be much easier for us to check for duplicate words. It'll be kind of slow for things like imports (which are already a lot slower in 2.0, unfortunately, with duplicate-checking enabled it could take a good 20-30 minutes to go through something like the HSK list) but should be fine for everyday card additions. 1.0-to-2.0 conversion will be a 2-step process, you run a little utility to dump your 1.0 cards to a 2.0 XML file (which includes score / correct % / flag / etc info and specifies the exact dictionary entries to link to) and then import that into 2.0 like any other XML flashcard list, so assuming we do offer a "remove duplicates" option in the 2.0 import screen, turning that on would let you get rid of those duplicated cards.
Sarevok - yes, there's no screenshot of the "display" settings screen but it lets you add a number of extra buttons to the flashcard interface, including one to delete a card, one to instantly change its score (so you could effectively "bury" it by multiplying its score by 10x or 100x), and one to add it to / remove it from a specified category.