This is "Camelot 30K" by Robert L. Forward.
The astronauts do not make themselves small, but rather build a small probe in the shape of one of the locals.
Out on the far boundaries of the Solar System, in the Oort Cloud, intelligent life has been discovered by humanity's space probes. Now the first humans to venture beyond the planetary system have been sent to make contact with this incredibly strange race and to tour the center of their civilization. What they discover is explosive beyond their wildest dreams.
The aliens call themselves kerack and the humans give them names from Arthur's cycle: the main alien character is Merlene, another is Launcelot. Queen Une's bodyguard is called Mordet, and the city-state is called Camalor.
The kerack spend their time battling with the neighbour cities so that the bravest souls may descend to Heaven. Heaven is a great chamber under the Queen's palace, and their souls are little round heavy pellets of uranium - because the kerack have a bio-nuclear biology allowing them to thrive at a mere 30 Kelvin, near absolute zero. Their one great racial achievement is the construction of Heaven, a carefully built semispherical chamber that, not accidentally, acts as a perfect neutron reflector. It is said that when enough souls have descended into Heaven, Camalor will ascend to greatness on a pillar of fire.
This is the scene of the explosion (and I found the reference to the hexagons, which I think is the only one in the book):
...stored under the altar, resulting in a large thermonuclear fusion explosion.
Surrounding the explosion was a thick cylinder of lead, surrounded in turn by the heavy metal contents of the privies. The inertia of this thick cylindrical wall of heavy metals constrained the explosion and directed the explosive force upward, where it struck the under-surface of the Palace o' Princesses under the Plaza o'Dance.
The Palace o Princesses had been fabricated of seamless black boron carbide, which was almost as strong as crystalline diamond and could withstand higher temperatures. The rooms in the Palace o'Princesses had been made hexagonal in shape, producing a structure that had the greatest strength for the least weight. As a result, the Palace o'Princesses maintained its physical integrity as the shock front of the thermonuclear explosion hit it.
The palace accelerated rapidly upward, driven by the directed thermonuclear explosion, until it and the cargo of spores on its upper surface attained escape velocity and were thrown into interstellar space.
"Faster, Hiroshi! Faster!"
Elizabeth was watching the view from the monitor camera on the pole overlooking the plaza. "The princesses have stopped bringing uranium pellets to the Queen and are sliding the doors back into place. Now I know why the doors had to be so massive."
Spurts of yellowish smoke shot from cracks around the loos, and a heartbeat later, the plaza floor rose as a single body carrying with it the piles of spores on its upper surface. There was a blinding flash of light, and the camera monitor over the plaza stopped working.
(Yes, yes. But as Robert L. Forward himself wrote in the preface, never lets the fact get in the way of a good story. This book required four or five times my usual level of suspension of disbelief, and I can only say that it was worth it).
The thermonuclear device