This is indeed puzzling. Some photos work and some photos don't. Since the problem started before your update to iMovie 10.1.6, the new version isn't the cause. So a reinstall is not likely to help. (Could always try, anyway.) Since the photos all import fine in iMovie 9, that likely eliminates any incompatible photo format problems as the cause. (Are there any differences in format between the photos that appear versus the photos that don't? If so, that might be a clue.) The Photos app itself doesn't appear to be the cause, since some photos from the app do import and, further, JPEGs from a Canon do not appear either. So far, I can't see a common thread.
Here are some random thoughts I have:
I take it you have tried dragging (not copy pasting or otherwise exporting) the photos directly from your Photos app into a folder on your desktop, and then from there dragging them into iMovie. If not, try that.
Also, you can try opening iMovie in a different user account. You can use the Guest account on your Mac for this purpose, or create a new one from the Users and Groups folder in your System Preferences.
You could try opening iMovie in a new or different library and see if that makes any difference. To do that, launch iMovie while holding down the Option key, and you will get a box that lets you select a different library or create a new library.
If you current library is on an external drive, check to make sure the drive is formatted for Apple (MAC OS extended, journaled). If you need to reformat, you will lose any data on the drive, so move or backup all data that you want to save.
Possibly trying to import in different projects might yield some more information.
If you still have iPhoto on your Mac, you can try importing from there.
With a photo that doesn't appear, try dragging it onto your desktop, opening it in Preview, and doing a File/Save As as a .PNG or TIFF file and see if that appears properly in iMovie. (To get the "SAVE AS" option from the File menu you need to hold down the Option key.)
Frankly, I am running out of idea here. As you mentioned, you can use Time Machine to revert to an earlier working iMovie version. Your work done in a later version likely will be lost. So keep the later version on your computer.
All else failing, you might try making an appointment at the Apple genius bar in a local Apple store, bring in your computer, and see if they have any suggestions or solutions.
Good luck with this.