It's not possible for salt to permeate the crystal and create inclusions. Your quartz is fine. The inclusions were probably there before you soaked it and you just hadn't noticed. (Quartz is 7 on the Mohs scale.)

OTOH, if the quartz isn't really quartz and is clear calcite (3 on Mohs scale), for example, then it's possible for it to soak up some water (after many, not a few, hours).

Either way, it's still usable for any purpose.