I dug into this with a couple friends this afternoon, and to the best of our ability it would appear there were simply no qualifying films for this year.
Here's the list of, at least current, qualifications for films to be eligible for consideration for Best Documentary Feature.
And here's a Wikipedia list of documentary films released in 1946:
Of the movies listed, only 3 have running times over 40 minutes, which is the required running time for a feature film.
- Criminales de guerra
- Let There Be Light
- Theirs Is the Glory
Let There Be Light was suppressed by the US Government and was not released until the 1980s, therefore any exhibition requirements would not have been met.
The other two films are British and Argentinian, making them very unlikely to have been exhibited in the US under the requirements outlined by the submission rules. I will admit this is speculation, but this was also a post-World War II environment so no release outside their countries of origin or outside their respective continents would not be beyond the scope of reason.
All other films on that list simply did not meet the +40 minute runtime requirement.
Naturally this list of documentaries for 1946 could be and likely is incomplete, but based on what research I was able to cobble together, this would seem to be the most likely answer.