Where did you find a systems preferences in App Store? It's always in the Apple menu anyway but has no connection to App store.
The matter regularly arises and Dah*veed has advised several times to re-index the HD.
umm..... I went to the App Store preferences in the System Preferences. I didn't see a setting that looked like it would help. I saw I could turn off the App Store from automatically checking for updates, but nonetheless, once an update is flagged for me to "do", if I don't want the update, then I still have the red number and an active request to perform an update. Someone tried to solve this a couple weeks ago.... I've have to go look at my post, but he suggested in older os there was a drop down menu if you double clicked on the update botton. This does not seem to be the case currently. Seems like a worthy oversight for Apple to fix. But currently, if anyone has a fix I'd love to know.