Download icon gone in Safari after update
The Downloads icon disappears when you clear out the downloaded items from the list. To make sure it stays quasi-permanently, go to Safari Preferences > General > Remove History items and set it to Manually.

This way, as long as you keep at least one item in the list of downloads, the icon will stay in the toolbar. Setting it to Manually ensures that the other settings - After one day|one week|two weeks|one month|one year - will not clear out the list without user intervention.