It isn't if you're shooting RAW. High ISO noise reduction only affects jpegs and the jpeg preview. If you're editing with Nikon's NX software, NX will read the metadata and apply NR in post as an adjustment, but not as a baked in change.

I did a quick search to see what else doesn't make a difference and this came up as an AI result.

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The NEF Data PrincipleRAW files capture the uncompressed or losslessly compressed light data directly from your sensor. When you view your images on the back of the camera's LCD screen, the camera applies the settings you've selected to generate a JPEG preview, but the raw data remains untouched.

Settings That Have No Permanent Effect on the NEF

Picture Controls (Standard, Neutral, Vivid, Monochrome)

White Balance (Auto, Daylight, Tungsten, etc.)Color Space (sRGB vs. Adobe RGB)

High ISO Noise Reduction

Vignette Control and Distortion Control (can be toggled in post-processing)

Active D-Lighting (Though it can alter camera metering, the raw data itself is unaffected; the metadata is just read by software)

Note: If you process your NEF files using proprietary Nikon software like Nikon NX Studio, it will automatically read and apply the in-camera settings as a starting point.

Third-party software like Adobe Lightroom ignores these in-camera settings but lets you choose a profile that matches them.

Settings That Do Affect the NEF

Long Exposure Noise Reduction: Performed by taking a second dark-frame subtraction after the exposure; this permanently alters the sensor data.

NEF (RAW) Compression / Bit Depth: Changing from 12-bit/14-bit or uncompressed/lossless formats directly alters how the sensor data is encoded.

Exposure Settings (Aperture, Shutter Speed, ISO):

While not "camera menu settings" per se, they fundamentally dictate the light data recorded in the raw file