Is it a right decision to directly disapprove something which we can not see by our eyes?

We can see ourselves or the objects surrounding us, since the sunlight of different colours is either reflected or transmitted by the atoms of our body or the objects. In reality, any object made of atoms with vibrating electrons is known to either reflect or transmit light of certain wavelength and therefore can be seen by our eyes. But, whatever we see is mostly not the actual mass or particles of an object, since 99.999999...% of an atom's space is empty. Anyway, can we rule out the possibility of existence of objects consisting of no atom or sub-atomic particles? Similarly as dark matter (in the center of a galaxy) which carries no atom or sub-atomic particles and prevents light emission by its strong gravitational force, our surrounding might have objects possessing their energy in different forms rather than being stored in atomic and sub-atomic particles. If they exist, will we be able to see them?