With 4000 nodes I needed to increase the neighbourhood from 8 (this image is with 16) to avoid the breaking/overlap as described in the blog post. I suspect an alternative solution is to reduce the node movement speed when I increase the node count, so that it is relative to the cell size.

With this high node count and speed there are interesting emergent dynamics with locally-dense pockets between less-dense regions.

But it doesn't run at a realtime framerate any more, my CPU takes 1m15s to simulate 1min at 60fps, before even doing any rendering. With rendering:
512x256: 47fps
1024x512: 46fps
2048x1024: 32fps
4096x2048: 8fps
8192x4096: 2fps

Reducing the neighbourhood count speeds simulation up enough to be realtime, but rendering is the bottleneck.