1. If both of these semicircular is one type of zone like solid or fluid, there is no need to merge them because both side of diameter have been meshed and ANSYS wouldn't recognize that as a wall. In another case ANSYS will recognize whole of it as one zone.
2. If you want to solve it in 2D like a circular plate, you could select just one part of it and solve it by using symmetry condition for diameter line. In this way achieving to result may take lower time.
3. If it's a sphere domain, you could use the diameter as a axisymmetric boundary type and solve just one part of this domain.
4. At last if you want to solve both these part, merging them after meshing will delete your mesh.So you should merge these faces by using merge option and mesh them after that.