There's not a lot that can be done to protect the mechanics of a game. Once you rename and reword all the cards, you're fairly free to do whatever you want. The visual design elements of a game can be protected, but dominion is not dependent on any of those.
This is why games like 'who is it?' (guess who) and '4 in a row' (connect four) can be made fairly easily. Scrabble has a protection on the board layout, but if you make a different board (see words with friends) and don't use the word scrabble, you're pretty much free to do whatever you want.
The dominion-shuffler apps would generally be violating the trademark, especially if they do not make it very very very clear that they do not allow you to play the game, and copyright if they actually include card images or rule text, but I don't think there's much reason for such apps to be pursued (unless an official app comes out and can't get to the top of the search results for 'dominion').
(Note: I am not a lawyer, so don't go crying if you do rip off somebody's game and get sued because I don't know what I'm talking about).