At this point, my guess for the motivation of using the test weapon on Earth is the Sphere Builders were desperate for any advantage. They might have decided any reduction and interference in the human population would have sufficient ripple effects in the future to warrant even a half assed attack. Every dead person in ENT, by the 26th century, could account for thousands of people disappearing from the time stream.
Roughly 1 million people were killed or injured. If they all died, then 6 billion people in the future could have disappeared.
Not necessarily. Because of the way genes are passed down, the odds that any given ancestor contributed any genes or chromosomes at all to your genetic makeup decreases the further you go back. After
just 5 generations, it becomes all but inevitable that one or more of your great-to-the-fourth grandparents will have no genetic relationship to you, only a genealogical one. After 10 generations, you'll only have genes from about one in eight of your ancestors. By 14 or 15 generations back, you're essentially getting no genes at all from those ancestors. From the 22nd century to the 26th is 400 years, which is about 16 generations. So removing those few million people from the timeline might have no genetic effect at all on the existence of any individuals in the Sphere-Builders' time.
Well, okay, the fact that they were all in the same area increases the chance that multiple individuals among them would've been part of a given descendant's genetic tree, though that's less true in the age of global (and interplanetary) mass transit than it would've been in the past. Also, some estimates put it at more like
1000 years before we run out of direct genetic ancestors. But
this article points out how rapidly our pool of ancestors grows until we can basically say we're all descended from everyone. The human genetic pool is finite and strongly intermixed, so there's a huge amount of redundancy. If an ancestor who provided certain genes is erased from history, they might just be replaced by a different ancestor who provides essentially the same genes, just a small part of the whole genetic code (as Poul Anderson proposed in his Time Patrol stories). After all, those ancestors will all have the same ancestors as each other if you go back far enough.
Of course, that's just genetics. It's possible that different people would perform different actions that would cause future events to unfold differently. But only in some cases would those actions be pivotal enough to have changes that amplified over time rather than being damped out by larger-scale events. For instance, removing Edith Keeler from history had a larger global impact than removing Rodent, the bum in the alley. But that would be more likely to change what events occurred than who was born. Sure, if my grandparents never met and gave birth to my mother, I wouldn't exist; but if two of my 32 great-great-great-grandparents had never met and given birth to one of my 16 great-great-grandparents, then odds are I'd still exist with maybe a couple of different chromosomes. At least one of those great-great-great-grandparents would probably have married someone else and still had a kid, right?
Which could go a long way toward explaining why so many of the same people exist in both the Prime Universe and the Mirror Universe. Although it doesn't explain why they keep ending up serving on the same ships or stations together.