All the data is stored in the nooki PDS. And there is one nooki PDS and can only be one PDS? Or can anyone make one?

Users have PDSes (Personal Data Server). Nookie wouldn't have a PDS, it could have its own database but that's not anything to do with the protocol.

The theory with ATProto is that user facing interfaces (App Views) write data directly to PDSes and then this data is aggregated by a giant index (Relays). This relay data is then consumed by those App Views that sort them into posts, replies, likes etc. and presents it to the user as a usable interface to interact with.

That's the high level gist, Bluesky is ridiculously over-engineered as it's made by a bunch of cryptobros who wanted 'social media but on the blockchain' originally and this bleeds into the wider ATProto ecosystem.

I can't speak for nookie, it could just be a basic centralised site that uses Bluesky as a sign-in mechanism. (That'd make sense given the apparent author prompted it here before and didn't say it had any ATProto integration and it used to have the ability to create accounts).

I'm not an ATProto expert either, but broadly speaking, it's more of an aspirationally decentralized service, a lot of it is still centrally run by Blue Sky. Rather than split all responsibilities equally among hundreds of equal peers like ActivityPub, they've broken up the responsibilities themselves into modular parts: one thing stores user data, one thing is a firehose of everything happening everywhere, one thing is providing content moderation, etc., and users can kind of assemble their social network from all the parts they like. Many parts of it were designed with the assumption that the whole thing would have to operate at Twitter scale (that was the original idea, to make something that Twitter could move to) so it's basically impossible for others to run some parts, like the firehose. The theory is that the real big infra stuff will all be so generic and neutral that there won't even a reason for people to run their own anyway, and the more subjective or personal bits like personal data or moderation decisions will be easier to host alternatives for.

Honestly? Neither am I. This post is mostly a trial balloon to see what people think about the abstract high level idea of potentially talking cross-protocol with BlueSky users.