Yes, but, consider this, Clark can still recognize people eye color, hair color and texture, just not the exact face features.
Batman has a differnt smell than Bruce, maybe because Batman suit it's difficult to clean so its exernal armor kinda smells like blood or Gotham streets and is washed like once a month and it gets dirty again the same night, and Alfred usually cleans like weekly the internal part of the suit. Bruce on the other hand usually smells nice, like the smell of the shampoo or some cologne and the armor blocks the smell of the soap he usually uses.
Plus the clow of the suit has white eyes and the hair is covered, in all of this Clark dosen't know that Batman and Bruce are the same person.
But one day, maybe because Bruce showered in the watchtower with the same soap he usually uses or the suit was just cleaned and still didn't go on patrol before the meeting on the watchtower, Clark recognizes the smell and just as an instict calls Batman Bruce (before the meeting room is full there are like 2 other people, J'onn and Diana, that alredy knows Bruce identity for one reason or another) and right there Clark realize that Batman, is Bruce Wayne
I love identity reveal fanfics, I will never get tired of them, but I would love to see some new spins like; Clark Kent actually has face blindness, yeah turns out Kryptonians use the sense of smell or something. I just think it would be remarkably entertaining to Face-revealed Batman to be having his Dramatic Moment. And Superman is just : ) hello friend <3 absolutely clueless