iPhone to Mac mini photos disorganization

First a warning: be sure that your external drive is properly formatted!  To avoid damaging the Photos Library an external drive must be formatted in either APFS format or Mac OS Extended (Journaled) format. Additionally, the drive can not have had Time Machine on it since it was formatted. There have been so many problems with using incompatible drives that the newest macOSs won't even allow a Library on a non-Mac formatted drive to open, since there is a chance of damaging the Photos database. See this:

Move your Photos library to save space on your Mac - Apple Support

To deal with all the pictures, I would open a new Library on the external drive, name it All Pictures (or something), and import all the old pictures to it. Use the most recent OS you are running.

In Photos File>Import, you can select another another Library, including iPhoto Libraries. It will present all the pictures, separate out any that seem to it to have already been imported, and ask if you want all the rest, or if you would rather select just some of them. So you could go though all your other Libraries, collecting the ones that Photos thinks aren't duplicates. And, of course, you can select folders of loose images, as well.

Duplicate selection is hardly perfect, but it is very helpful. In macOSs 13 and 14, duplicate detection is available after import, as well (though it will take awhile to scan its Library,) and you will need to look through its list for pictures that are similar but not exact, and see if you want to keep both.

Be careful not to try to bypass the import process-- there may be old pictures, videos especially, that are not compatible, and you want to give Photos a chance to catch them.

Dealing with "Hidden" pictures has changed with the OSs-- "Hidden" used to mean for a particular album--now it means for the picture, itself. So a picture designated as hidden is hidden everywhere.

I hope this helps-- let us know...

Videos are, in general, crazy. The encoding of videos seems to change without warning, and ".mov" doesn't always mean the same thing. I have recently tried to round up videos from all over different backup drives from current and previous decades, and I have had to swap among 4 different conversion apps to make files that could be played-- and some never worked. Are these videos playing on your phone?

You haven't said which version of iOS you are using on your SE. Does it have a Files app? If so, I would save the video to the Files app and try to export from there. Then you could use Mac apps to deal with them.

5GB of iCloud storage is free. You could save the video files to iCloud and import them from there.

I'm afraid I don't remember the details of how "Hidden" pictures worked in Sierra, and then I only would have used it on the Mac. Have you done a forced re-start? This will describe how-- it's different for different phones and for different iOSs, so you will need to set that on the page:

Force restart iPhone - Apple Support