During high-velocity intercepts (at least 50 km/s) frame rate drops to less than 1. Sometimes even for low-velocity intercepts in certain circumstances. I am supposing that this has to do with the patched conics system and how the game calculates multiple SOI changes.
A setting to control how many SOI changes and their corresponding trajectories are calculated would probably vastly increase performance. I believe Kerbal Space Program 1 supports between 1 - 6 or 1 - 8 patched conics modes. The higher the mode, the more SOI changes and trajectories that are calculated and displayed.