For example, shadow ball used to be physical but lowered the target's special defense. Shadow ball is the only one I know. Please don't question my curiosity.
Well actually there is no other move except shadow ball. In gen 1-3 shadow ball as you stated was physical while it lowered the sp. def. The only 2 other notable but not quite the same examples are of acid and crunch. Acid was a physical move and hence lowered the defence back then while crunch was a special move which lowered sp. def. However as you know both moves' categories were basically interchanged in the later generations with corresponding effects. So yeah no other move than shadow ball. Hope I helped. :)))