Why did I lose my NEF files, and could only find small JPEGs in their place in the Recycle Bin?

It sounds like what you found were the JPEG preview thumbnail images that are part of NEF files. Raw files for just about every camera maker include more than just the raw data collected by the sensor. They also include metadata that records things such as camera settings and meter readings, as well as preview images (that can be full, half, or quarter size of the sensor's resolution) and much smaller thumbnail preview images generated by the camera's raw conversion engine using the in camera settings in force at the time the photo was taken.

As for 72 dpi, that's pretty much meaningless for a digital image unless it is imported into a program, such as a page setting application or a document creation application like Word, that pays attention to the dpi number to determine the size of the image as it is embedded in another document. The vast majority of image display applications and even current printing applications will scale digital images to fit the amount of space provided, regardless of the dpi number in the EXIF info.

That rather sounds like preview images generated/extracted by your file system explorer. However, it would seem to be rather strange that they should be found in the trash rather than getting straightforwardly deleted when no longer in use since the trash is really intended for files by the user.

You don't even bother to say whether you are missing your NEF files on a memory card or on your system disk. If it is the former, the most likely culprit is removing the memory card from computer or camera while it is being written. If it is the latter, it's more likely to be an overall disk failure. There are recovery programs for either problem. And either problem should have been covered by you by timely backups: it is never a good idea to have personal files on only one device for extended durations without backup.