My perspective on physical reality has changed and grown so much since I first wondered that, and yet the answer as to why crystals can effect us and why they form the perfect surfaces comes from the same principle.
We all pretty much understand about the different phases of matter:
gas (molecules bouncing all over, little order)
liquid (molecules sliding around, still moving fast, little order)
and solid (molecules vibrating in place to form a condensed object that we see as solid matter)
(By the way, this would be a picture of an amorphous solid, such as glass or the wood of your desk)
Well, when something is in its true crystalline form, the molecules have lined up into a perfectly ordered structure based in part on the charges of the atoms that make it up.
For example, Celestite is strontium sulfate (SrSO4, meaning each molecule of the celestite crystal is made up of one Strontium atom binded together with one sulfer atom and 4 oxygen atoms).
The way this molecule is put together, there will be certain areas that have a positive charge, certian areas that have a negative charge and certain areas with no charge at all--this is what dictates how these molecules of the celestite crystal prefer to line up with each other to form a crystal lattice (because, remember, positive likes to line up close to negative, areas of no charge like to be near other areas of no charge, etc.)
A crystal lattice
Looking at these pictures helps me to understand the answer to my childhood question: how can a crystal form these perfectly smooth glass-like surfaces on its own? Well, it is extremely ordered on a molecular level and if you keep adding billions of molecules in a perfect structural alignment, eventually you will be able to see the object's pattern with your eyes and it will carry that same order and structure, which can include very smooth surfaces or crystal faces.
Now, how does this tie in to why crystals would have an effect upon us in the physical world? Well, many of us are now understanding that everything in our world is energy, or vibration or frequency. We also have the principle of resonance: sound waves make objects vibrate in a similar manner. This is why you can hit one tuning fork and have one untouched but near it also start to produce sound. This is also why the most talented opera diva can sometimes hit a note that shatters glass!
So, if we believe that everything is energy and vibration in the physical world, including our bodies, our brains, our neurotransmitters etc, it would make sense that we could possibly resonate with the vibration or frequency of a physical object on some subtle level. Well, what object would you expect to have the most powerful, pure, amplified, unified vibration? The gas, liquid or even solid object without a crystal lattice structure (called an amorphous solid, an example is glass). NO! You would think that something possessing a crystal lattice structure would have the most magnified, pure vibration and have the most chance of having an affect upon our own vibration!
Voila! that is how I have made sense of crystals, on a very general level. there is much more involved and I am always thinking and trying to learn more, but this is a good place to start. I don't think it is a good thing to just believe what people tell you in this world, especially people who want your money! It is best to ask questions and think for ourselves. Do crystals effect us as living systems? Yes, there are studies that prove this which I will go into at another time. But the above is my working vision for WHY they could affect us!