"You are very beautiful, too."

Not exactly sure what you mean but "çok da" would be "very too" which doesn't make sense in either language. This sentence is about "you, too", that is, "you, too, are very beautiful", which closely resembles "sen de çok güzelsin" in its structure.

I wonder how we could express this: you are very beautiful and very smart, too. In other words, you are not only very beautiful but also very smart. Maybe this is where "hem de" comes in? Sen hem çok güzel hem de çok akıllısın?