I have a D800 with a Vello grip and Nikon batteries. No issue whatsoever with how the batteries discharge. In my experience there are two types of "3rd Party" manufacturers, those that produce at a price point and those that produce at a quality level. I've been consistently happy with the Vello products I've purchased as I have with Sigma. Certain products, like batteries, have sufficiently documented issues when used with other aftermarket products that I would never consider buying 3rd party (though I have a pair that were throw-ins from other purchases). I've read of many other manufacturers of batteries, grips and other things that people buy because of price and they are routinely plagued by issues. That doesn't surprise me in the least.
Is Nikon "manipulating" software to purposefully screw with 3rd party gear? I don't know, but if I had to guess I would say that there is no intentional manipulation going on, but neither is there any thought into how changes in a new camera might impact 3rd party product developers - it's just a matter of making the new camera work. Why do I think this? Because Nikon isn't smart enough to build consistency within its own menu systems. Go from one camera to another and look through the various menus and you'll find nothing is in the same order, even with cameras as similar as the D7000 and the D600. Heck, they even switch the order of function buttons on the back of cameras making it mind-numbingly difficult to shoot with two different models at the same time without screwing up something, or at a minimum zooming out when your wanted to zoom in. They don't screw with 3rd parties, they screw with their own customers.
You can be as conspiratorial as you'd like - that's what the internet is for, right? Evidence suggests otherwise. With all new technology the existing technology needs to adapt or die. That's all this is.