How do scientists know the structure of other planets in the solar system?
We can also use things like radar (radio waves) to 'see' beneath clouds.
Most gases are transparent to radio waves allowing us to determine the structures that are normally invisible beneath the clouds. The same is true for other wavelengths such as U.V and infrared to some degree.
The details are complex, depending on what the clouds are made of, but in essence we get a reflection from a sudden change in density (e.g gas to solid) and this can be detected by an orbiting spacecraft or a powerful telescope.