How do aircraft brake when using skis?
You may find this manual of interest from the FAA. The short answer is that they don't have brakes like wheeled aircraft do. With sufficient runway you don't need brakes to stop a wheeled aircraft either. The airframe often provides enough drag to stop the airplane. You are generally correct that aerodynamics are not the primary method of braking, however they can in some cases be sufficient. On top of that ski operations are often flown from a frozen lake or similar area where there may be a great deal of unobstructed distance for takeoff and landing.

Some types of skis let the wheels poke through them for both snow and hard runways. In some cases the wheels may contact the ground beneath the snow and allow for traditional braking or they may be plowing through the snow providing drag.