The Boolean tools are provided to help create geometries that cannot be created any other way.
DesignBuilder Support recommends that you only use them for this purpose only and avoid the temptation to use the union tool simply to reduce the number of blocks in a model.

As a general guide, it is usually better to work with a number of simpler blocks than one block of complex geometry. The more complex the block geometry the more challenging the generation of the zone inner geometry and the more likely that DB will generate surfaces of zero thickness.

One specific case that sometimes leads to zone inner volume creation failing and surfaces having zero thickness is when more than 3 surfaces are adjacent to a vertex. This is more likely to happen with blocks of complex geometry. It is not such an issue for EnergyPlus simulations because DesignBuilder is still able to account for surface thickness when calculating zone volumes and floor areas, but it can be a real issue for CFD which requires any internal surfaces to have non-zero thickness.

Note that the zone merge tools are the preferred method for creating zones spanning multiple blocks.