"Digging" a hole in the cloud layer is a great suggestion by Ulco. I do that too sometimes and it takes a bit of fiddling to get the hole in the right position. This is how I usually do it:
1) create a new camera and have it look down on your landscape from great altitude
2) disconnect the current density shader of the cloud layer and
3) replace it with a distribution shader
4) create a simple shape shader (texture position) of a soft circle, set size to the size of the hole, like 500x500 meters for starters.
5) use the simple shape shader as blend shader and choose to invert it.
Now there are 2 ways to find the spot of where to put the hole in the cloud layer. Do it by math (sun angle etc.) or by eye/fiddling.
Math is mystery to me, so I choose the fiddling
6) From your new camera high up right-click in the terrain where the sun needs to shine directly on the surface and righ-click to choose "copy coordinates"
7) paste the coordinates in the simple shape shader
re-render preview and see that hole in cloud is away from that position, as the sun has an angle and direction.
The lower the angle the further it's off.
9) move the simple shape shader in the direction of the sun's direction
10) if the hole isn't well visible then set cloud density and edge sharpness to 1 and make the simple shape shader hard-edged.
11) Once you have pin-pointed the coordinates then re-connect the density shader for your clouds and don't forget to change back your cloud density and edge sharpness settings if you did change those.
12) Use the simple shape shader as blend-shader for your cloud density shader.
13) If the hole is too harsh then make the shape softer
14) If you like some variation, instead of a clean clear hole (omg, ambiguous talke here), then reduce the white of the simple shape to a grey value, like 50% grey.
A lot of steps, but actually not so much work!
You can also do this in an empty scene to make it easier.
Then copy/paste the sun from your project into the empty scene and repeat the process.
Instead, then try to make the sun shine directly at the origin 0,0,0 and measure how far the simple shape shader deviates from those coordinates.
Use those values to add/subtract them from the coordinates you measured in the 3D preview from your project file.
