In my document I used images which are now gone (files were deleted) but yet they are still in my document. When packaging the document, InDesign says links are missing though. I don't understand this, if they're missing (I know they are) then how come they are displayed in the document? And what can I do if I don't remember where I found them initially?
The files in your InDesign document are previews of the images you placed. You can't retrieve the originals from within your InDesign document if you deleted the original files.
To prevent losing or accidental removing images, its best to work with versions and to package each version.
I am not familiar with inDesign too much, but you could try the following in case you initially found the picture on the Internet...
Take a screenshot of the pictures in your document and use Google Reverse Image Search to find similar or the exact same picture. In case you got it from the Internet, you are most likely to find it doing so. Here is an article on how to use Google Reverse Image Search.