Is it safe to modify the SInputEvent and SInputSymbol structs in IInput.h? I was looking to modify them by adding Vec3 and Quat fields in addition to the standard value field. Would this dissrupt anything else in the input system?

yes it probably would crash since you can't recompile the rest of the engine. Simple rule is don't change any I*.h file unless you know what you're doing (and there isn't really a reason to do so don't).

Best way to extend the Events is to wrap them again into a new input listener queue with your own structure again.

Just something new and don't change or delete what's there. It'll be fine if there aren't any conflicts.