Shimano Sora 9-speed shifters "missing a speed"
I'm kind of confused here. You say you can only click 8 times. On a 9 speed bike, there would only be 8 clicks for shifting.  Let's say you start on the largest gear, and we'll call that 1.  Clicking 1 time with bring you to gear 2. Clicking 2 times will bring you to 3. Clicking 3 times with bring you to 4. Continuing on with the pattern will bring you on to clicking 8 times to bring you to 9.  

If you bike was skipping a gear somewhere in the middle, you would shift 7 times, and already be on the smallest gear, and shifting one more time would bring you nowhere, as you would already be at the bottom. The limit screw would keep it in it's place, and the cable would go a bit slack. Going up the cassette you would notice a problem where you still had 1 click left, but would be unable to move the shifter because you would be pushing against the limit screw.