I don't think I'd go as far as to ban them entirely. I think malduk had a good point when he said the decision of what to up and what not to up is part of what would make partially upped cards interesting.
If nothing else, I wouldn't ban completely them just because there are some decks that specifically want unupped cards.
I think were the issue comes in is how to make it so that some teams aren't at a huge disadvantage just because they don't have members with a huge number of upped cards. I suppose as long as people were required to give the number of upped cards they have accurately, this could be seen as part of the auction, ie players that have a large number of upped cards will be more valuable because of the options they have available.
Another option is just to not allow upped towers/pends. I think this is the area where most people fall short. For example, I have about 600 upped cards, but I'd be surprised if I had more than 200 pillars/pends. On second thought though, maybe it wouldn't be too big of a deal because most of the time you only really use quanta sources from your element anyway, and buying 15 of each of those afterwards wouldn't be too hard.