I decided to rewrite my answer after a bit more thought.
The complexity of your problem is not O(N^3) in the worst case, it is actually only O(N^2) in the worst case. It's also not O(N*M*K) but rather O(N*(M+K)), where O(M+K) is O(N). However, the real complexity of your problem is O(E) where E is the total number of logical connections (number of work connections + number of parent connections). Unless you want to approximate, your solution cannot be better than O(E). Your averages suggest that you likely have on the order of 5 million connections, which is on the order of O(N log N).
You example uses two sets of logical connections. So you would simply cycle through each set and check if distance between the devices of the logical connection is within the threshold.
That being said, the example you gave and your assumed time complexity suggests you are interested in more than just if the individual connections are within threshold, but rather if sets of connections are within threshold. Specifically, in your example it would return True if parents logic: (A,B), (A,C) and Work logic (A,C),(A,D),(A,E),(A,F) are all True. In which case your best data structure would be a dictionary of dictionaries that looks like the following in Python (includes the optimization below): "parentsLogic[A][B] = (last position A, last position B, was within threshold)".
If it's common that the positions don't change much, you may obtain some run-time improvement by storing the previous positions and if they were within the threshold or not (Boolean). The benefit is that you can simply return the previous result if the two positions haven't changed and updating them if they have changed.