I believes she actually split some of the original Take Mikazuchi's soul to form the 8 Noxes we know. The remaining half was kept in Taka Mikazuchi and became known as a Nox Nyctores form then on despite existing before hand as a remnant from the Age of Orgin (Phae Shift 2). Take Mikazuchi's soul though was composed of human souls though, but the details are unclear how they were composed.
In That Which is Inherited, Kokonoe does uses Nine's spell Infinite Gravity during the artificial identity smelting experiment during the Ikaruga Civil War to unwittingly restore Nirvana's core and complete the Wave Weapon/Detonator (Relius' take on Nox Nyctores or Phenomenon weapons in the same vein that the IDEA engine and artificial causality weapons ares Kokonoe's non-magic/non-seithr based take on the concept) Ignis. So Nine was fully capable of harvesting human souls, its just Taka Mikazuchi had large and strong of enough soul to shave off that was easier to harvest (lets be real, Nine would totally do it if it meant that Celica wouldn't be in danger of having to be the fuel?/switch for Taka Mikazuchi).
Someones else can clarify further.