I did a quick search of the US Copyright Registry to see if Konami registered the copyrights. I found at least one for the actual cards, so I would assume if their attorneys filed for one set, they filed for all.
This means that Upper Deck is open to additional damages. Under US Copyright law, there are two measures of damages that the Plaintiff (copyright owner) can choose from. one is a measure of lost profits and damage to the business of the plaintiff, the other is statutory damages. These statutory damages increase significantly, up to $150,000 per violation, when the plaintiff can prove willful or knowing infringement.
The statute also allows for recovery of attorneys fees.
My guess, without seeing any of the filings in the case, is that Upper Deck admitted to the willful and knowing infringement to save substantial legals fees. If you read the article, it indicates that Konami was pursuing the lost profits measure of damages. This requires very costly surveys and audits.
One more thing to consider is depending on the copyrights that are held, each one of the individual cards may be a separate violation. Even if the number of violations is 10% of the total cards printed, that is 6,000 violations. Do the math, 6,000 violations at $150,000 per.
With the amount of game used memorabilia that Upper Deck has purchased and cut up but has not included in cards, I sure hope that they try to reach a settlement agreement and continue making cards. I would hate for the hobby to lose at that game used memorabilia.