BoardSim needs a logical pin in order to add any type of model. So if the solder beads are implemented as components then you can assign a model. They are probably one-pin components, and that presents an obstacle, but you can possibly work around that.
If the solder beads are designed only as solder mask geometry then there is nothing logical to tie to a model. You would then need to export the net to LineSim, find the solder bead location in the free-form schematic, and add a capacitor at that point.
Another idea is to define a 3-D area around the solder bead, edit the geometry to include the solder, and solve it in the full-wave solver. This would calculate the effect of the solder bead and automatically put the model into the net. See this short video about creating 3-D areas: https://support.mentor.com/knowledge-base/MG592355