For HTML5, you can use the 'hidden' attribute.
<option hidden>Hidden option</option>
It is not supported by IE < 11. But if you need only to hide a few elements, maybe it would be better to just set the hidden attribute in combination with disabled in comparison to adding/removing elements or doing not semantically correct constructions.
<select> _x000D_
<option>Option1</option>_x000D_
<option>Option2</option>_x000D_
<option hidden>Hidden Option</option>_x000D_
</select>
_x000D_