1) Duh. Anything over a reel qty will obviously be shipped as a full reel. I mean I guess you could order a full reel's quantity as cut tape, but then it's you being stupid.
Not necessarily. There are at least a couple distributors for which the only way that they will guarantee you a full reel is if you order them in full reel quantities and only full reel quantities. So if you need 5000 PCS and the reel size is 4000, you have to order a reel of 4000, and a separate cut tape and/or "digireel-like" order for the remaining 1000, at whatever price break applies at 1000.
And yes, I've had this experience. The specific one I am thinking of seems to never ship full reels unless you say you have to have a full reel OR order exactly a full reel quantity.
2) Unacceptable. Because this can (and apparently does) happen... Your 2000 will be split up into 1 piece (but it's a traceable 1 piece! Yay!), and 1999 pieces... A reel with 1 part on it is objectively stupid.
It's much bettter than getting 10 bags each with anywhere between 20 and 500 in each bag. Or worse, them all poorly spliced together onto a single reel.
The problem with the "single tape piece" method is that the distributor ends up with lots and lots of odd-length pieces, and then some unlucky person gets all of the dregs in one order, or the distributor eats the leftovers. If you want to have fun, go and order every last piece of a certain part from a distributor which doesn't do what digikey does - you'll usually end up the "10 bags" I described above.
If I know I'm getting exactly one or two reels for all the non-reel quantities in my order, even if on occasion one of the reels has a handful of pieces, I'm ok with that, especially if I know I'll NEVER see more than 2 partials if they use this method.
I totally get the ridiculousness of how this appears. On the other hand, once you start digging into traceability and anti-counterfeiting methods which are having to be done to avoid counterfeit components making it into critical electronics one starts to realize that a consistent methodology is required for robust supply chain traceability. Having a pile of different-length trimmings that you then have to sort through to find the best one to cut another piece off to send to a customer is anything but consistent, and is going to be very difficult to keep the traceability intact. So you have to come up with a method that can be used for every order no matter what the quantity. The method I described where you ship full reels and then a maximum of two reels is consistent, repeatable, ensures FIFO, and yes, has the disadvantage that the customer gets two separate reels fairly frequently, and sometimes gets a ridiculously small quantity on one reel. Remember that digi-key sells to companies who need traceability, so they have to use methods which enable them to do so.
It would be nice if you could specify something like "splice all my extras onto one reel". Or, specify some minimum qty you'll take if they get down to a ridiculously small quantity on a separate reel. For your example order, there is a good chance that I personally would have been fine with a single reel of 1999 if they sold it at the qty 2000 per-piece price. If the 1999 on the "partial" reel, and when they counted them they discovered they needed a single one to get to the 2000 you ordered, then leaving the 1 part off isn't unreasonable if you agree to this. Likewise, if the 1 pc was the leftover part, they should have either just gifted that to the previous order, or tossed it (unless it's expensive enough that it's more than what a re-reel costs). But all of this requires judgement and complicates the fulfillment process which equates to more, better-skilled employees which are really hard to hire and keep anymore.