Table to Points with hexagonal points?

Is there any way to plot 2D hexagons in Table to Points?

In a word, no.

Table to Points cannot construct topology connections (such as which 6 points form a hexahedron) simply because this information is not in the table.

If there is some custom implicit arrangement of the points in your data, you could possibly write programmable filter to generate the connection array and build a poly data or unstructured grid. Alternately, you could change your data source to supply this information. I presume that you are storing your data in something like a csv file, but there are several simple file formats that can express polygon connectivity (ply, stl, vtk).