Issue seems like it would be the need for a breakwater or ships large enough to weather inclement weather and the occasional rogue wave.

The great junk armada would sink rather quickly.

Again, limited to locations that are already sheltered bays or have some other structures providing this shelter. Under normal sea conditions a lashed-together collection of ships will grind each other to bits. This is why oil rigs can't often have anything docked to them. They use cranes to move people and equipment from boats. Naval ships setup cable shuttles to move people and goods between ships. It's possible that some locations on the sea --in some strange future weather conditions-- may remain so calm as to allow ships to safely dock to each other for long periods. But the first storm to come along would quickly destroy them. Snow Crash seems to have been borrowing on the folklore of the Sargasso Sea whose large patches of seaweed were once said to trap ships and bind them into strange communities of the lost. This was often depicted in old adventure literature, comics, and fantasy art. But it was just myth. Sargasso weed is very light and while it gathers together in gyres like plastic trash, it is also constantly being broken up and reformed.

There was once a proposal for a Sargasso-like marine settlement based on the principles of a colonial organism, composed of dwelling pods, energy 'animals' with deployable wind and solar, fish pens, and other special floating modules linked together by a web of cables and always digitally aware of their relative positions. Using parasails for propulsion, it would gather its parts together closer when the sea conditions were calm allowing gangways to be used --trying to travel mostly in the 'doldrums' along the Equator-- but would spread out over a larger area to avoid collisions when the weather was rough. The catch with this idea was that dwellings were like the escape pods used by oil rigs and people would have to put up with a very rough ride every time the weather turned poor. However, such a concept might be combined with 'sea tower' designs using SPAR buoy structures that were more comfortable, but very difficult to fabricate or repair at sea.