I thought it would intelligently integrate the JPG file into the .NEF file structure so that I could treat them as a single unit.
When you save a raw file, the camera almost always incorporates a jpeg preview into the raw image file's data. This occurs whether or not you save a JPEG file as well as a raw file. JPEG images often also contain smaller thumbnail preview images, although this is not as universal as jpeg previews embedded in raw image files.
The image files (raw or jpeg) usually contain a lot of information in addition to the actual image data. EXIF information and other metadata are included. One or more preview images can also be included. Depending on the camera, built-in jpeg previews may have a resolution lower than or equal to the camera's native resolution. Many cameras also include a miniature jpeg file at very low resolution. So, even if you can extract a jpeg preview from a raw file, the resolution may not be complete, it may be heavily compressed, or it may have another quality that may be considered undesirable as the final image.
Is it one of those situations where something like Lightroom is beneficial for this workflow, or am I missing something in the way the two can work together rather than just as they seem to me at the moment to be "too much information"?
The use of Raw + JPEG has the advantage of not having to extract raw container preview images from raw files if you are satisfied with the way the camera has handled the Photo. Most raw processing applications do not include the ability to extract preview images as standalone files.
Apart from the manufacturer's internal software, most raw processing applications do not apply the "in camera" settings to the raw images. Thus, even though the JPEG preview uses the camera's processing engine and the raw conversion application can use the built-in jpeg format to allow you to quickly preview the image, when you export an image derived from raw image data, you will not get the same result. results as an integrated preview. It can be close or radically different. It all depends on the default settings of the raw conversion application.
I do not use LR to edit / delete images. So this is not a complete answer to your question, but I'm pretty sure that there are user-configurable options in LR to link the two separate files when they are reviewed. When you mark, for example, the JPEG file as a "two-star" image, the corresponding raw file is also marked with a "two-star". Professional digital photo offers such an option. I have never used the Nikon ViewNX, so I can not say more about the options available.
With LR, you also have the option to choose from the following options: when previewing images, display embedded preview (faster) or wait for LR to render raw data with the help of default development of LR. Once again, from Canon DPP also offers similar options for reviewing raw files, but I can not speak for ViewNX.