I say “yes” a lot when I reward. I agree, it’s a bad habit. I think I got trained to do it because Bodie used to bite hides ALL the time. I used it to draw her attention away and bridge her reward. On the plus side dogs that bite hides do teach you to reward really fast and at source! Fortunately she is rather independent and stubborn, and I don’t think it hurts us. But I do believe that there is no up-side to using a marker.
I also worry that calling “alert” in practice could become a conditioned reinforcer. Then when you false alert in blind searches I wonder if that can confuse the dog. Again it’s something I often do anyway, and my food crazed Labrador thinks it’s only the cookie that counts, so no fallout (yet).