The only way to know what they have is to get one tested, an avian vet can send of blood work and other tests. Or if one dies you can have a necropsy done by a state lab.
Other then that, there are many different respiratory diseases chickens can get, many are viral, some are bacterial. Antibiotic's won't help if it's viral. The problem is that viral diseases can easily and quickly morph into bacterial infections if chickens are very congested and have a lot of junk in their airways. So it's a choice you'll have to make regarding antibiotics. If you hear heavy wheezing or rattling breathing it's probably a good idea to treat. Once they get pneumonia it's hard to bring them back.
Whether or not they continue to have problems with this from now on depends on what they have. Some diseases create a carrier state that can flare up repeatedly, others run their course and you may never see another outbreak. This is why testing is very helpful.