Tbph, I think this is technically one of the least problomatic ships in the series, outside of the whole enemies to lovers thing, especially since they're both likely immortal so at the very least they now have each other.
And after finding the journal entry again while it does heavily imply she outlived her partners through shear age, we have to remember the world they live in is ABSURDLY dangerous, so there's a non zero chance that at least one, if not all of them, met their end some other way.
One of the more prevailing theories I've seen is that Hornet is only in her 50's or so in the first game, which is just enough time to witness the plauge twice. Another is that they have actual bug life spans, we're just seeing it from their perspectives, which actualy would make the whole immortality thing an even worse prospect for them.