From the looks of it, most of the current Quincy were born in a quite modern times on earth (the hospital that "Y"s were born looked quite modern). They were simply the "chosen ones" 9-18 years ago, while all other that were not chosen, had their powers stripped off and absorbed, except for Uryu. Though I have to wonder when Souken exactly died (maybe it was 9 years ago after all), because if he were indeed recognized by Bach as strong pure Quincy, then there is no way that a bunch of hollows could own him, rather it would make more sense if at that moment he lost his powers like Masaki. The other possibility is that the whole Ishida line is resistant to Bach.
Of course, let's not forget that Souken did communicate with other Quincy to some point, after all he did throw away their achievements, as mentioned by Opie.
By shooting condensed reishi, they annihilate the soul, or most of it's parts at least. It might be more akin to a sum of "+" and "-" giving "0", or simply that condensed reishi completely annihilates the target without leaving any remains to move on (the spirit does disappear and lave an empty spot in the balance).
I have to also wonder about the reason that Time-Space Kidou is forbidden and that might be perhaps that type annihilates the souls instead of cleansing it, thus destroying the balance that Shinigami themselves are meant to preserve.
Also, does the Shinigami themselves count into the balance ? After all, when a few 1000 Hollows were destroyed in Human World, Kurotsuchi had to eliminate a similar amount of Rukonagi people, but when a few 1000 Shinigami died in the attack, nothing happened to the balance (unless it was taken care prior to the attack by the Quincy ?) ? Unless most of those Shinigami survived, but are simply no longer in combat ready state.