I'm hardly a lore expert, so maybe there are good in-univerese reasons they are cubes. But if you think about ships being assembled organically, I'd expect a more spherical shape once you get past a certain size.
It's been a long time since I've seen any of the movies, but now that you mention it I do seem to recall that spherical ship... Now I wonder if there's a tetrahedron borg ship out there somewhere
In this case, I'd still expect more like a cylinder, but I love the idea! Borguccini? Borghetti?