You are asking if we create such exact simulations of humans that they will have all the typical limitations would they have the same wants as real humans, probably yes.

I'm also asking, should we care?
More generally, I'm asking what is it about real humans we should prefer to preserve, given the choice? What should we be willing to discard, given a reason?

The original question Wei Dai was asking me was about my statement that if we becomes uploads "At that point you already lost humanity by definition".

Fair enough. I've already agreed that this is true for the definitions you've chosen, so if that's really all you're talking about, then I guess there's nothing more to say. As I said before, I don't think those are useful definitions, and I don't use them myself.

Does the fact that somewhere in the cyberspace there is still a piece of source code which wants the same things as I do makes a difference in this scenario?

Source code? Maybe not; it depends on whether that code is ever compiled.
Object code? Yes, it makes a huge difference.

I still feel like humanity gets destroyed in this scenario, but you are free to disagree with my interpretation.

Some things get destroyed. Other things survive. Ultimately, the question in this scenario is how much do I value what we've lost, and how much do I value what we've gained?
My answer depends on the specifics of the simulation, and is based on what I value about humanity.

The thing is, I could ask precisely the same question about aging from 18 to 80. Some things are lost, other things are not. Does my 18-year-old self get destroyed in the process, or does it just transform into an 80-year-old? My answer depends on the specifics of the aging, and is based on what I value about my 18-year-old self.

We face these questions every day; they aren't some weird science-fiction consideration. And for the most part, we accept that as long as certain key attributes are preserved, we continue to exist.