Hello PROBERT1968,
Currently there are no tools in Metashape to detect the clouds on the images. But you can apply the masks manually - masked areas will be excluded from the depth maps, texture and orthomosaic generation procedures automatically and can be optionally excluded from the image matching procedure.
As for marker placement, it is not recommended to put marker projections on the point that is not clearly visible, as it could affect correct estimation of the related 3D location.