It seems that when there are any large linked images present, Illustrator locks up for several seconds or more before the Save Adobe PDF dialog appears. Often the delay is long enough that I end up switching to another task while I wait.

This never used to happen in previous versions — I believe the problem started with an update in late 2018 or early 2019. Based on the delay before the dialog appears, it seems like Illustrator might be refreshing/re-reading the images in the background, because the delay seems to increase with more/larger images.

All my working files are saved on a very fast NAS, so I tested my theory by watching the performance tab in Windows Task Manager. Sure enough, ethernet spikes while Illustrator locks up. However, I don't think this problem is related to the files being loaded/saved over ethernet, because I often experience the same delay on my Mac at home when saving PDF files from Illustrator. On my Mac, all working files are saved on my internal SSD, yet I still get the same long delay when large images are present.