In all the 3D modeling I've done, There are two ways the mesh is generated, in triangles or in quads (square). prior to that, geometry is stored in point clouds (an array of dots)

By connecting those dots, which define points in a 3d space, you create a mesh.

a Triangular mesh is more efficient, but not always as smooth.
a Quad mesh can provide better curved surfaces, but usually takes up more space file-wise.

The more points you have, the more quads or triangles you have, the higher the resolution you end up with, but it can have the downside of taking up more memory, or taking longer to slice the model for 3d printing.

I can think of two ways the hex pattern is used in regards to the grid:

1: it's a throwback to tabletop RPG gaming, most miniatures in a tabletop game, and some pc games, have their movement regulated by a hex grid. a map will have the terrain divided up by a hex grid, to allow a player to determine how they can turn, fire their weapons, and move. look at Battletech for an example of this.

Seeing as how ENCOM started out as a game company, this makes sense, as a hex grid may be at the core of the layout of the Grid; Perhaps recycled code from early game projects? a hex grid allows for a smooth definition of range of movement, turning radius, etc. Their system is unique and proprietary, isn't it? Maybe they broke the mold in this regard.

2: the other time I see a Hex associated with 3D models is when I slice a model for printing with Skeinforge (a slicing engine). When you generate infill for a model, in most slicers, it generates a square infill grid with alternating threads of plastic along the x and y axis. In Skeinforge, it generates a honeycomb lattice infill (a hex grid). this provides greater strength, and generally uses less filament, and takes about the same amount of time to print. Perhaps this is why you see it used in the Grid. It's advantages over a square or triangular grid outweigh it's complexity / use of system resources.

As was said earlier, you see the hex in nature, like in a honeycomb. Maybe the underlying complexity of the system itself led to the creation of the ISOs. Perhaps an ISO couldn't come into being without the unique ecology of Encom's proprietary system. In other words, they couldn't come into being on other platforms, but in the unique structure of the Grid, it was a given.

Just my thoughts.

Have you checked out the "signature" design for the Tron Legacy/Evolution/Uprising concept design artist Daniel Simon?