CP, I agree, you're spot on. Maybe his angle was to appeal to card collectors by selling the red decks normally, and appealing to DB general fans by offering the signed decks. I also would have bought the set had the box been signed and the cards left alone. A custom seal on the box and decks with matching numbers would have been fine too so that it couldn't be said that it was just a random signed box with two decks thrown in to create a "Limited edition" set.
A few years back, I bought a set of his posters, all autographed. They were $10 more each than the un-autographed ones. When I bought the original black Split Spades, back when he was at his peak of performances (During the Frozen in Time era), and you could get an autographed playing card added to your order for an extra $10. Although I don't perform, I do a lot of research into magic and like knowing how to do all of the street magic type of tricks just for fun. There's not a lot that I can't easily figure out. That said, DB is my favorite performer because of his showmanship, audience control, and how he performs the tricks. That's where his talent is, and I appreciate him for that. I have his performance posters hanging in my office, as well as at home, as well as autographed items. His fame is still great, but he has passed the peak of the greatest hype for his career to this point. If his autograph was worth an extra $10 way back when, I can't see it being worth more now, especially with that many more autographed items available for purchase.
I also note that he stated that only 1,000 decks would be SOLD (my emphasis) on the site. Sure, he could use some for personal performances, but he most likely still has many past decks that could be used as well. Maybe there will eventually be items on the website where a red deck will be included "free" with purchase of something else.
I don't see it making a lot of business sense to (Let's assume the numbers are as such) produce 2,500 decks, keep 1,500, and sell the other 1,000 when you could have easily produced 5,000 and sold 3,500. That's a lot of extra income even if you only factor in $5/deck profit (It's most likely a lot more). Who doesn't want to make more money? At the very least, donate the extra earnings to charity.