I wrote the original version of the npm registry in a day or two on top of CouchDB. I built it quickly and didn't think much about scale.
Isaacs continued to improve and maintain that code. At one point he even wrote up an open standard for generic js package registries for CommonJS but they didn't seem to care (they were too busy arguing about promises).
At the time I wrote the initial code I was employed at CouchOne and we had a small CouchDB hosting platform operated by Jason Smith which is where we ran the registry free of charge. Later on, after CouchOne was aquired by Membase and became Couchbase, it decided to break off the hosting company and give/sell it to Jason Smith, which became IrisCouch.
IrisCouch continued to run the registry for free for several years. They had no venture funding and limited resources but they provided this service for our community anyway. They announced a product for enterprise (hosted) NPM but as far as I know it wasn't really marketed or sold. Last year IrisCouch was acquired by Nodejitsu.
Nodejitsu continued to host the registry for free. Some time last year the infrastructure hit a breaking point, mostly around CouchDB. Remember, I wrote this in a weekend when less than a hundred node packages existed. Many of the semantics from me and Isaacs' initial "prototype" persisted until just a few weeks ago. For instance, this single database held all the package binaries, for every version of a package, attached to the document for that package.
Once the registry started to have serious stability issues a few things happened. Isaacs started to work on ways to improve the reliability by changing how the registry worked and Nodejitsu sought community support for keeping the current registry up. At some point Isaacs also decided it would be best if he worked on NPM full time and built NPM Inc.
In the early days we weren't thinking about 58K modules, that was just crazy, we were just figuring out the simplest way to store a couple packages the node community was writing. Since founding this company Isaacs has already managed to re-write the way the registry works to fit the kind of load we have now.
Nodejitsu is now free of the financial burden that was dragging them down as well and Isaacs' new infrastructure can keep the registry up more cheaply than the previous system and more reliably.