Actually, I updated thanks to reading this paper by Bostrom, so I gotta rephrase stuff.

First, two identical people living in separate simulations are just as much separate people as any other separate people are separate people. It doesn't matter if there exist an identical replica somewhere else, the value of this person in particular doesn't decrease tinyest bit. They're distinct but identical.

Second, uniqueness of their identity decreases as there are more people like them, as you described with option #2. However, this property is not too interesting, since it has nothing to do with their personal experiences.

So what we get is this: Simulations together hold 100x our experiences, and we're either offered a deal that kills 99x of us, or the one that 99% certainly kills us. Both have same expected utility. On both cases, we cease to be with 99% certainty. Both have the same negative expected utility.

But the interesting thing happens when we try to ensure continued flow of us existing, since by some magic, it seems to favor A to B, when both seem to be perfectly equal. I'm kinda feeling that problematic nature of handling divergence comes from irrational nature of this tendency to value continued flow of existence. But dunno.