Why are F(ab)2 fragments used in preference to whole IgG for the manufacture of conjugates?

There are two main reasons. The first is that the F(ab)2 fragment will bind more specifically to the target; that's a natural function of the protein just being smaller than the full-length IgG. However, in addition, the Fc region of the IgG molecule has a number of effector functions (like complement activation) which are distinct from just the IgG binding to its target. Without the Fc region, the IgG conjugate is less likely to cause problems due to these effector functions.