Software to assist drawing of complex, three-dimensional skeletal formula from scratch or from existing crystal structure
Thanks to vapid and their comment


  There are editors that have 3D mode and they can display a 3D molecule in 2D manner. MarvinSketch is first that comes to my mind, but there are probably more.


I figured a crude solution, which I hope might as well serve as a starting point for other answers.

First of all, I completely forgot that MarvinSketch (free (registration required), available for Windows, Linux, macOS) has support for 3D.
Drawing in 3D from scratch with MarvinSketch is probably not the best idea as even though it has a support for optimizing (cleaning) 3D structures, it sometimes gives weird results for organics and practically not suitable for inorganic complexes and especially clusters.

Arguably, the best and the most affordable third-party tool for creating such structures is Avogadro (open source, available for Windows, Linux, macOS).

If there is a crystal structure at hand (e.g. CIF data), then one must do two things first:


crop/grow the fragment of interest;
assign proper bond orders and export the structure in one of the formats that preserve bond orders (such as MOL, MOL2, PDB or CML). 


I believe Avogadro can do both, but I personally like to do part 1 in Olex2 (free (registration required), available for Windows, Linux, macOS) by force of habit.

As a proof of concept, I took the crystal structure for the trefoil knot, allowed it to grow from assymetric unit to a complete molecule as well as cut out solvent and guest molecules, so I was left with the initial shape:



which I immediately exported to the MOL file by running file trefoil-knot.mol.

Next, I opened this MOL file with Avogadro, which automatically assigned bond orders:



and the file was exported to MOL once again, and subsequently opened in MarvinSketch (I reduced fog in settings, made implicit hydrogens hidden and used F7 button to align the molecule on screen):



And the final result came out to look like this:



The image is, however, not quite as perfect as the one in the paper.
For instance, there are some artifacts about inflection points as if the program was confused how to place double bonds.
Also, if you look closer, the grayed out part which was supposed to be further from the viewer, actually appears in front, which I attribute to the fact that Marvin was designed as a 2D molecular editor first and foremost, so it doesn't always handles depth (or the aforementioned z-buffer) adequately.