I've never heard anything but supposition that Nikon will deny warranty repair based on third-party battery use. I've heard people say third-party batteries are more likely to cause damage but Nikon batteries are the only batteries I've heard of having been recalled due to manufacturer defect. Not too mention I find it HIGHLY doubtful Nikon manufacturers their own batteries; it's far more likely their manufacture is outsourced and Nikon maintains in house quality control standards. Now if someone feels better putting a Nikon branded battery in their camera, fine. If you sleep better at night because of it, great. But I don't see how a third party battery is much different than using a third-party lens or a third-party flash. I think all this arm flailing is much ado about zilch, personally.
Secondly, in my experience some of the third-party batteries out there equal, if not exceed, their Nikon branded equivalents. The Wasabi batteries I use in my D7100 are and my GF uses some in her '3200 with equal success. Remove the label and you'd never know you weren't using a Nikon branded battery. My current 9-5 job is, and for the last 14 years has been, working in the Visual Arts division at a college; I have regular, ongoing access to several full-time professional photographers and the department has several loaner cameras of both Nikon and Canon manufacture for student use. I see requisitions for that area for third-party batteries with some frequency. No issues with them. The professionals I see every day, a lot of them use third party batteries, a lot of them don't. No one really seems to care. When I asked them about battery preference (OEM vs. third-party) they all pretty much said the same thing, "(shrug) It's a battery...
"I'm not saying there aren't some pretty crappy third-party knock-off batteries out there because I know there are; I've owned a few. But to paint ALL third-party batteries with the same broad brush is simply inaccurate and misleading. Rampant fanboy-ism is fine, cute even (to a point), but don't quote what amounts to opinion and supposition as though it came to us engraved on stone tablets handed down from On High. The simple fact is, there ARE some excellent third-party batteries that cost a fraction of a Nikon OEM battery.
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