Does anyone sculpt their models in clay?

Does anyone sculpt their 3d models in clay and then scan them into 3d?

is there a way to control the topology of the model with lines drawn on the clay model?

You might find this article interesting:

Pixar does

you might find this handy in your case to turn a 3d scanned model to a quatface
youll find there a free retopo tool.

There are other retopo tools too usually not free goolge them.
The above one is a bit hard to find if i didnt gave you the link.

And the tool does allow you to to draw lines on your modell, which then the mesher tries to follow. (as you wanted)