The question is, worth more money still in the crate or if you get her running and put some miles on the clock?

As an 883 and has been in the crate this long, I see no good reason to take it out. Museum piece, dealership decoration etc.

Lots of guys claimed they bought them in the crate and stored them during the anniversary year. They seem to be hitting the market. But are they worth anything?

 

Myself, I wouldn't hesitate.

 

But it's not really a new bike,it's been sitting for 20 years and I would venture it'll need much more than just new tires.
Also an actual new bike comes with a warranty not a list of possible headaches not covered.
It would not surprize me to hear that this bike when it gets started and ridden a bit starts leaking oil from dried out seals and I'd have concerns with things like wheel bearings with 20 year old grease in them all dried out or dry rotted brake lines etc.
Sitting 20 years is unkind to any machine no matter how low the mileage.
Just Say'n.

 

And the joke was on them,many were ordered a year or more in advance to be sure and get that special anniversary model,then when they came out every bike they made that year was an anniversary model so there weren't and special anniversary models just 2003s with a 100th badge on the whole line up.

 

My own bike was 9 years old when I bought it with 8,000 miles and had sat in a garage for almost 3 years. The brake lines and hoses are fine. The PO put new tires and battery on to get it ready to sell. The EFI was gunked up, I dealt with that myself.
If a new one is 11K and this one is 8 it leaves a little budget for some new parts. Plus it has the carburetor and solid mounted engine, being an 883 they don't vibrate as bad as the 1200s. You're right though, I guess it ain't "new."