I agree. I too believe that this lack of side hull armour on the Type-99 tanks is a deliberate decision. These tanks are expected to be fighting in traditional armoured formations. Where flank protection can be covered by wingman tanks and other units. These tanks are not intended to fight in urban battlefields like Grozny or Fallujah. Since the PLA's doctrine is mainly defensive, there is little need to play the occupying force where urban combat becomes much more common.
Anyway, additional side hull armour is heavy and bulky, thus impacting mobility. If they are not needed, why have them bog down your tanks. We can also see this logic with the other top tier tanks in East Asia. The Type 10s and the K2s. These tanks too generally lack side hull armour in their current configuration. Even the Abrams did not have that impressive side hull armour until they experienced Iraq in 2003 onwards. After that, the Abrams begins to get the TUSK package. Hence, I believe the manufacturer could quite easily have a 'TUSK' package for the Type 99s on the catalogue. An add-on package just in case they these tanks do need to go into urban combat.
Some of the loudest voices that I have heard bashing the Type 99 for its lack of hull side armour are from the War Thunder players. They think that by driving a tank in a video game, they have suddenly become tank experts. This is laughable. For example, a tanker in War Thunder could target and snipe out individual 'weak points' of an enemy tank. But a tanker in real life could only make out an enemy tank's profile on his FLIR at 1800m out. He could hit the enemy tank, but he won't be able to pick out which part of the tank he wants to hit. Not to mention the other 'game balancing' things that distorts the realism even more. Hence, War Thunder is not real life, and we should not take it too seriously.
Honestly having reinforced roof armor might actually prove more useful than side hull armor, especially with all the talk about swarms of drones (or at least large numbers of them). True, a layered ADS network and especially having won air superiority through the use of fighter jets will eliminate the threat of larger drones such as GJ-2 or MQ-9. But for the small and low-flying drones that are harder to detect, the threat is not as easily eliminated, especially in more urban environments where they can literally fly out of a window, go several hundred meters until it is vertically straight up above your tank, and drop an AT bomb in similar fashion to this:
Granted, first image is an extremely small bomb that probably did negligible damage, and second image is not on a tank (but it dropped a far larger bomb, and the M1 could have been the target instead). I don't believe PLA is actually going to lose tanks to improvised DJIs, but they definitely still pose a threat. IDF also had to deal with similar threats from Hamas. And of course, the threat of top-attack ATGMs or self-targeting munitions such as CH-901 or Switchblade will also necessitate reinforced roof armor, as it has already been established that APS cannot be relied on 100% of the time. Lastly, the threat of artillery is another major tank killer. Of course having a strong enough roof to survive a Smerch or even Grad rocket is out of the questionable, same goes for guided conventional shells such as Krasnopol-type munitions. But a roof strong enough to withstand hits from a standard battalion-level infantry mortar should be the minimum at least. Believe it or not, more than just a few tanks in Donbass and Syria were unlucky recipients of an 82mm straight through the turret roof, with terrible results.
That said, 99A seems to have some sort of reinforcement to the turret roof (possibly ERA?), and they don't look like simple bullet breakers. ZTQ for sure has ERA on the roof, and it seems to be heavy-ERA also which is a plus. But not enough for the 99A even though it probably also is ERA, and IMO if it was one or the other (and especially so given the doctrine), spending the weight on a reinforced roof is preferable to having reinforced hull sides.