To use grayscale or color documents is the same under operator profile. But you have to consider: the increased amount of informations to manage and the requiring of transformation.
The grayscala and color images have a greater quantity of data respect to monochromatic images: if a black and white image of an A4 page scanned at 300 DPI has 1 Mb of data, the same image in grayscale has 8 Mb of data and the color version has 24 Mb of data ! So you have to use well sized hardware resource when you plan to use this kind of pages and you have to consider a decrase of global speed.
Some time, based on kind of data to recognized, the system requires to transform the gray-scale or color image in black&white so that the recognition engine can process in the right mode the data: in this case the transforming operation could introduces noise on the image and the result could be not as expected. This is a reare case becouse there are used state of art thresholding algorithms, but you can investigate on this event if the performances are not as expected.