The problem is bad motherboard design, and (without knowledge of your model) you could be being led down the garden path by the repair shop. You might want a second opinion from a shop that works at the chip level if its not a warranty repair. (If you are in a country with strong consumer protection laws you could be covered under fitness for purpose laws).
At a wild guess the drive may have gone faulty, drawn to much current and destroyes something, or static electricity (esd) may have been the cause.
What you are describing is very rare - most failures ive seen in this regard limit damage ti the USB port. There is no way to totally prevent the risk, but a quality powered hub ir docking station cpuld act as a sacrificial part/filter in some cases. Migrating to USB-C may also theoretically offer some protections.
It may be worth reading up (googling) "USB Killers" - usb sticks designed to kill systems - as the mechanism - ie a high voltage pulse eminating from a usb key - is very possibly analogous to what you experienced, and examples typically show ports blowing up, with better made devices limiting damage more.
Was the drive powered externally as well or USB powered? External power to different ground, etc. could've caused some electrical issues.... – ivanivan – 2019-06-27T17:45:29.493
No external power – ps0604 – 2019-06-27T18:08:02.303