In my experience, it's more common to have navmeshes that take into account agent radius than account for agent radius in path planning. The main reason is that treating agents as a single point greatly simplifies (and therefore speeds up) path queries as you suggest. Even with non-circular agents, it's often sufficient to use a circular or cylindrical approximation of the agent's shape for the purposes of pathfinding or navmesh generation.
To handle varying-sized
agents, you can quantize the range of radii to a small set of sizes for which you can build separate navmeshes. An agent then just uses the navmesh that most closely matches its radius. It's more data to bake and load for a level, but the lookups are usually still faster than incorporating agent radius into pathing or doing full movement planning for every agent.
All that being said, every game is different and it may be advantageous to take one approach over another for a number of reasons.