USB standards change power delivery depending on the socket type, and USB-C has the most changes, but the theme is the same on all of them: Provide a given amount of current, and if too much is drawn, it will have either an
active fuse (which shuts down, but doesn't require replacement when power and sink are restored), or else a
polymer fuse (they are fuses which have a polymer that melts when it gets hot enough, and breaks the power delivery; then, when it cools, the fuse self-restores, though it might take a long time, e.g., you
might wait a full day to use it again).
When you get a message about over-current, then it can be from too many devices on the cable. Most HUBs pass the power delivery requirement from all devices to the host PC. An active/powered HUB has its own power supply, and increases the amount of power available, and so if you have an active HUB, then the only possibility of the host PC itself seeing an over-current is if the wiring itself is bad (or perhaps if the HUB reports over-current, but the power available goes up on an active HUB).
It would not be unusual for what
@hedwar2011 mentions to be a problem: The motherboard or some part inside the chassis can short, and this would never recover until the short is removed.
Keyboards and mice and most joysticks don't use much power (the force feedback versions do, but they are externally powered). Headphones would not normally use much power either. Cameras and external drives use significantly more power. The higher the resolution and scan rate of a camera the more power it will use, but I think hard drives use a lot more power. If you don't have devices which consume a lot of power, then wiring seems to be at fault. One tool to debug is a powered HUB, which removes power delivery from the PC and hands off that requirement to the external power supply. You can place devices on an externally powered HUB and see if it solves the problem.
It is unlikely for a USB over-current to destroy the motherboard due to the fuse arrangement. On the other hand, if there are shorts, then perhaps USB was just one symptom of a wider problem.