Use Nuke's Scene node to set the display to 'off' or Atomkraft's 'AtomReadAsset' node that can load in the geo as points or bounding boxes for viewport display and then render them fully at rendertime. Simply export the instanced spheres as Alembic format and read them back in.
https://atomkraft.hk/docs/atomkraft/nuke/html/AtomReadAsset/index.html
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