Heya BluesMatt,
Try going to display properties and changing your Windows theme then switch back. Right click on desktop -> properties -> appearance. Also, try going to the advanced settings in the appearance tab and switching to large icons, then back to regular icons. Also maybe right clicking on your start button then going to properties then changing your start menu and switching back.
Hopefully one of those tries to reset your icons.
As far as how that happened, that is definitely strange. Possibly bad sectors or maybe malicious software. The only thing you could do on purpose to massively remove icons is to use the unused icon manager or just selecting a bunch of them and then deleting them. Which I doubt you did
Hopefully one of those things works. Can you still explore those icons if you right click on them then click explore? Or try double clicking them.