Why aren't my pictures really deleted from my iPhone?
One reason for finding some of the deleted photos could be because of the nature of iPhone's flash memory on which the data is saved - deletion or overwriting data is a slow process on such memory. So data in a flash memory are constantly moved to optimize it, and when you delete any file on it, it may not be deleted immediately but moved and marked for deletion later. (More here - Permamnently deleting on SSD).
So, while ios and Photos app may not show you the file on your iPhone or iPad  after you &quot;delete&quot; it on Photos, it may still be in the memory till it is actually deleted. That could be one reason why you are able to see them when you mount the iPhone drive on Linux. (I am speculating here because I don't know how you are mounting your iPhone on Linux and accessing its data).
The duplicates could be because of edits you made to the photos or photos you took in burst mode or HDR mode.