I am the author of [4].

Regarding your first question:

ZigZag is not really intended for large shared multi-user stuff. It's not supposed to scale huge. We have completely different data structures for translit (i.e., the hypertext part).

ZigZag can be used for fast manipulation of spacial relations (basically, applying multiple kinds of projections to a multi-dimensional directed graph) & we use it under the hood for representing display layout in XanaSpace, but its main use is as a personal mind-mapping utility. It has only extremely tenuous connections to how we do hypertext, and none at all to micropayments.

The transcopyright system (i.e., the thing for ownership and micropayments) is based on transclusion. Basically, all that means is that we provide facilities to fetch things piecemeal, and we provide facilities for owners to restrict control over getting usable forms of things. (Specifically, we support applying a one time pad, so that if you've got distributed fetching of real content, you can still require folks to fetch the OTP from a trusted oracle & maybe pay for it too before they can actually decode the data.)

Question 2:

We can always fall-back to byte offsets. We floated the idea of supporting more user-friendly offset formats for audio & video (specifically adopting ideas from the w3c media fragments spec), specifically because audio & video have complicated compression schemes & finding safe frame boundaries requires deep knowledge of the underlying format. We put that on hold in order to focus on getting text stuff really solid in the UI department.

Question 3:

People can create spammy documents. They can also transclude from or link to more popular documents in the hopes that their low-quality documents will get more exposure. But, links are not universally resident (which is to say, creating a link to a document doesn't mean that everybody viewing that document immediately sees it). Instead, links get distributed the same way as documents do: by word of mouth (as people recommend to their friends to view particular documents or load up particular sets of links). Links do double-duty as connections between documents and as formatting information (like themes or skins), and collections of links (ODLs) can be passed around separately from documents. (By 'passed around' I generally mean that their addresses get circulated, although we also had the notion of an archive format for passing around collections of documents and links that weren't to be made generally available.)

In other words, the spam potential of linking between a popular document and a low-quality document is akin to the spam potential of creating a low-quality website that is hidden from google.

Question 4:

A cell is a data structure consisting of a pair of associative arrays (pointers to adjacent cells, keyed by strings) & a 'value' (typically a string).

Cells are created by the author (or maybe by a program), which is fine, because cells never travel beyond the vicinity of a single machine. (We had a 'slice' mechanism where cells owned by different folks could join up together, but this was never intended to scale beyond small groups.)

Again: since ZigZag is not a part of the hypertext/transliterature system, the performance of ZigZag is a lot less important. (Within the translit realm, we had exotic high-performance data structures during the Autodesk / XOC era, which we've basically dropped in favor of simple stuff like spanpointers.)

If you're interested in ZigZag, I recommend reading my implementation (https://github.com/enkiv2/misc/blob/master/ds-lib/ZZCell.py). It's cleaner than GZZ & is almost identical to what's still used internally at Xanadu (last I've heard), because this is a rewrite from memory of what we wrote for XanaSpace & when Ted occasionally sends people to me for advice on how to implement new versions of ZigZag I point them to this.