On my 2011 deluxe edition optional cards, I see an asterisk on some of the cards, but nothing indicating it should be taken out of play. Should I assume that this is what is meant by the asterisk?
I have the same edition as you, and noticed the same thing. It looked to me like they just didn't have room at the bottom for the reminder.
I guess if you want to be sure you could post the specific cards. Alternately, you could compare them to the card list at twilightstrategy.com. The site is very thorough, so I doubt they would have any cards incorrectly starred.
On my 2011 deluxe edition optional cards, I see an asterisk on some of the cards, but nothing indicating it should be taken out of play. Should I assume that this is what is meant by the asterisk?
They should still be taken out of play if played for their event. For some reason, it's not stated on the cards in so many words.
In the rules only the asterisk is relevant (2.2.4) so yes, take out of play. The reminder to do that has just been missed. At least you do not have the original optionals as these did have several errors unfortunately.