Rendering a 50k-node dependency graph without melting the browser

WebGL + instanced rendering for nodes, plus a quadtree for hit-testing, is exactly right. Do not try to make SVG scale, you will lose. Render edges as a single buffered geometry, not per-edge objects.

For layout, run the force simulation in a web worker (or precompute on the Rust side since you already have one) and only stream positions to the renderer. Blocking the main thread for 30s is what is killing your UX, not the draw.

Sigma.js / a WebGL graph lib might save you the two weeks if your interactions are standard. Roll your own only if picking/styling needs are unusual.