In the case of metal nanoparticles (Au, Ag), agglomeration drastically changes the optical properties of colloidal solutions due to the plasmon coupling. This coupling changes not only the far field response, but also the near field optical properties. In the interparticle region there is an enhancement of the electric field. In some cases, aggregates are better than isolated nanoparticles for sensing applications. See the articles below.
ACS nano 6 (4), 3441-3452
The Journal of Physical Chemistry C 117 (44), 23090-23107
in pharmaceutical formulations, agglomeration calculation is one of the criteria to know the formulation stability. As agglomeration increases, the formulation becomes unstable and also the particle size and other properties also changes. so for developing a successful formulation, agglomeration calculation is mandatory.