Modelling wise you will most likely end up with inverted normals. This may cause invisible/missing faces or an inverted in-side-out model effect, with unexpected material shading. This can be easily fixed in edit mode by selecting all faces and flipping them or recalculating them with Ctrl+N.
Cycles is mostly immune to inverted normals in most regular materials, but it may still give adverse effects under certain situations when materials use normal maps or vector normal input.
Negatively scaled objects may also adversely affect certain simulations, like physics, fluids, smoke, certain modifiers, and/or constrains and rigging, that read or rely on object transforms.
Other than that nothing intrinsically wrong with it, it is the only quick method to invert an object after all.
If you no longer need the object to be an instance of other, or it is already an isolated object data user, then you may apply the scale with Ctrl+A > Scale.