Summer152, it is not so much that they need to "breath", but closed up you are taking the chance of them getting moist and then they can get a fungus and anything like that will take the luster off them. I don't even like the organza bags as I think they are abrasive feeling. I like nice soft cotton bags. After all pearls are basically secretions (spit) from live creatures. It is not like they are minerals or stone. Minerals can also degrade, some of the softer ones especially. Treat your beads and things tenderly. Also using a damp cloth to clean them is best because you do NOT want to get the silk that they are strung onto wet. The wet dries between the pearls, but inside the holes it stays wet longer and can begin a rot problem............then one day you are wearing your gorgeous pearls and they totally fall apart off the string. Ugh.
Imitation pearls are worse as they are just a coating on top of a plastic or glass bead.......then any moisture can get under the coating and all of a sudden you have a plastic bead necklace instead of your pearls. That happens a lot with vintage costume jewelry that has been jammed into jewelry boxes for years......... abrasions and moisture cause much damage to them.
And, yes ANY perfumes or skin products or lotions should be applied first, let them be absorbed or dry a bit then put on your jewelry. Many a nice piece of costume jewelry has been sprayed with perfume and both the finish is damaged and imitation pearls ruined and worse, they now have a coating on them and can and will collect dust and dirt from wearing, thus needing more cleaning.
This is an old thread but information on pearls and the finer beads and stuff is always pertinent and good to educate newer forum members. Donna