I don't know if they have changed anything in the last update.
Prior to that, bombing HQs would result in a high chance of leader losses. In 41, this favored the Germans. By mid-42, the Soviet have the advantage as the new bomber's come on line. They can literally destroy the German leadership structure by the end of 42 and never look back.
The recommendation is: 1) don't put HQs alone in a hex, 2) most players adopt a houserule limiting HQ bombing (the most common seems either 0 or 3 per turn), 3) even if you have a house rule, unless you manually use your entire airforce, they will sometimes bomb enemy HQ so you need flak.
How much flak you put with your HQs is really up to you. As the Soviet, I try to put one PVO regiment per HQ. Overtime, this protects my leaders but increases the German air losses way beyond what my early Soviet AF can do. Now, this depends on APs, Admin Pts and manpower - but its what I try to do.
For the Germans, in 41, I ALWAYS stack my HQ with somebody if possible. And I rarely assign them flak except at the Corps HQ level so that they commit to combat. But that's my perference given the ineffectivnesses of the Soviet AF until the first blizzard.
This doesn't directly answer your question as I haven't seen anything on this issue since the last upgrades. But its the best I can offer.
Hope this helps!