The description states that these cubes have an energy output of 5 kilotons of TNT, which is nothing to scoff at but it's not something spectacular either.
In fact 1 kg of Uranium-235 has an energy output of 17 kilotons and is much smaller than the Ion Cube, as in the form of a cube it would only have a volume of around 52 cubic centimeters. So it would have a width of around 37mm x 37 mm x 37 mm, so yeah it would easily fit in your palm. For example the bomb that decimated Hiroshima burned less than 1 kg out of the 64 it was packing as the blast had around 15 kilotons. So yeah it's not much really, I mean if it was 5 gigatons (5000000 kilotons) that would be really something.
The problem is made infinitely worse due to the existance of the Doomsday Device which is stated to have enough power to destroy most of the solar system and is around the size of an Ion Cube. By "most" it probably means it would not be able to destroy the main sequence star as that would require a whole different level, as a star would just adapt to any energy applied to it.
So I assume the Doomsday device has the energy output around an average Supernova which is around 24-48 octillion megatons or 24000-48000 octillion kilotons of TNT. So for simplicity let's say it has an output of 25 octillion megatons, that would make it's energy output 50000000000000000000000000000 times greater than that of the Ion Cube.
So yeah the Ion Cubes must be some inexpensive thechnology of the Architects if they can pack a lot more energy into an equally small item.