Missing Photos

The most likely reason for this is that your library is partially "referenced" (the library contains only pointers to photos stored elsewhere and low-resolution versions) rather than fully "maintained" (meaning all photos are actually stored in the library[1]). This would happen if the "Importing:" preference "Copy items to the Photos library" was not checked at the time some photos were imported.

You can see which photos are affected by creating a Smart Album like this:

If you retained the photos on the memory cards and you kept track of which photos are on which cards, you can "consolidate" those photos (copy them into the library) by selecting some and using "File" > "Consolidate...". You may have to do this one card or part of a card at a time.

Note [1]: When I say "stored in the library", that means either stored in the library that's on a local disk or stored in an iCloud Photo Library connected to your local library and possibly optimized to save local storage. "Referenced" photos are never copied to an iCloud Photo Library.

There are a number of folks who still mourn iPhoto and/or Aperture (which eventually converged their library formats but not their interface or functionality. I still keep both around, but I no longer keep that library updated, and I can't recall the last time I needed to refer to it. It is of course your decision how long to hang onto it.

Most of the issues that I ran into with Photos (after the first release or two) arose from trying to operate it as if it was just an update of iPhoto or Aperture, rather than a new program with new design goals and new paradigms.

discusduo wrote:

Ridiculous to import or drag from photo cards without indication of storage issue. Why? [...] I don't really want my desktop photos to run like a phone.

I'm not sure I understand either of these comments well enough to respond to them.

How can I verify photos are downloaded into the library rather than referenced at the time of download?

I can think of two approaches: Either continue to check the Smart Album to make sure it shows no new photos or just check the "Copy items to the Photos library" option and leave it that way. Photos has never worked well with referenced photos and does not provide the tools that Aperture did to resolve issues associated with them.