I'm not a Safari Bookmarks user so I can't report if things changed with any update. I see only a generic 'world'/'globe' icon in my Bookmarks list. (I'm surprised to even see so many sites/folders in my Bookmarks list! I have no idea who, how or when they were added/created
) I assume those original site icons are what you are calling 'lost site icons'?
History does show unique icons, but that list only last about a week or seven days (whichever comes first). Frankly, I've never cared for 'icons', especially after file titles lost the 32 character limit and especially tiny icons.
They are marginally useful in Safari tabs. I have 42 tabs open right now and only 10 unique icons are visible. On the other hand, not even all the tabs are even visible at one time. Of course, most of this problem is because I don't use "Full Screen" viewing of any app
; hardly any app I use needs the full width of my 27" monitor.
I'm sure my ramblings have been so helpful!