You may be interested in [this post][1].
Some possible suggestions...
1. Create individual GameObject instances
2. Use GPU instancing shader
3. Use a particle system and programmatically create objects as particles. (You can render with 3D meshes)
4. Programmatically create single meshs (or submeshes) that contain geometry for multiple spheres.
5. Use GPU geometry shaders to create 3D spheres from a point topology mesh.
[1]: https://forum.unity3d.com/threads/most-efficient-way-to-display-large-scatter-plots.403702/
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