Update: Unfortunately this calculator no longer appears to work.
When constructing your own hives it is useful to remember that wood shrinks and expands in relation to the moisture content of the wood. This means you might want to leave a little extra room for bee space if you expect your wood might become drier during use than it currently is.
According to the site If you are using kiln or air dried lumber you are probably in the area of 7 - 19% moisture. In North America it's typical for the moisture content in unfinished wood to fluctuate between 4 - 14%. So plugging those numbers for dried wood into the calculator, estimating about 1 cm of change in the depth of a hive box seems reasonable.
This is relevant to take into account as frames are made with the grain running parallel to the direction of the wood grain in hive bodies. So hive bodies will shrink and frames won't.
Note: the 'relative humidity' and 'moisture content' labels on the link seem to be reversed at the moment of writting this post. As each option allows different number ranges you can check you have selected the correct option by entering 101 for 'initial Relative Humidity or Moisture Content' and take note of which option the subsequent error message thinks you have selected.