Disk not ejected notification after ejecting disk properly

I always wait for the external drive's activity LED to stop flashing before I physically disconnect the drive from the computer. If the external drive does not have an activity light, then I wait at least 30 seconds for macOS to flush the cache and give the physical drive time to finish writing data. Unfortunately Apple removed the notification that told users "It is now safe to disconnect the drive". If you still get messages even waiting 30 seconds, then wait even longer...I would think a minute should be enough time. Otherwise you either have sort of issue with macOS which is interfering with macOS letting go of the external drive, or the external drive may have some sort of issue.

Hard drives will definitely take longer than SSDs to complete flushing the buffers as they are slower mechanical devices. Even some USB sticks may take a while as well since many USB sticks can be even slower than a hard drive.

APFS file system should not really be an issue here.

macOS itself can sometimes be the factor if the system is overloaded or the user is using anti-virus apps, cleaning/optimizer apps, or third party security software which may be slowing the system operations which will also slow the flushing of the buffers.

Even on a pristine Mac, I would wait at least 15 seconds before unplugging even when ejecting an SSD just to be safe.

This article may or may not be helpful but it seems to cover much of the same issue you are reporting:

Why do I get "Disk not ejected properly" … - Apple Community