Why not? In physical terms, the only reason that you may not want to put them to close together (e.g. in the same pouch or box) is for its esthetic appearance. You may want to place or wrap them separately in order not to scratch or break any of them.
In terms of energy, crystal can be stored together. It is in fact, great to store them together. There are crystals such as calcite, kyanite, selenite that are self cleansing and could also clear the energy of other crystals that are place together with them.
Unless the quantity of your crystals is high and you intuitive feel that the energy is too strong or creates discomfort, you are free to segregate them.
Also See ‘Working with more than 1 crystal’
