No, that's not right. It's as I told you at first.
When you do
binaryImage = grayImage < 128; % Find dark pixels. Dark = true, 1, white.
you're creating a matrix that is "true" wherever the image is dark . If you sum that, it treats the "true" pixels as 1, and thus, counts them - counts the dark pixels. So you're getting the sum of the "true/1/white" pixels in the binary image which means your getting the count of the dark pixels of the gray scale image. Doing it your complicated way would count the bright pixels. By the way, if you wanted the binary image to be false where the gray scale image was dark, you'd flip the less than sign and then sum the inverse, which is much simpler than doing the multi-step process you did.
binaryImage = grayImage > 128; % Find bright pixels instead of dark pixels.
numDarkPixels = sum(~binaryImage(:)); % Notice I had to invert the image with~.
