In poultry, there are general and specific clinical symptoms for certain diseases and disorders. A farmer must be conversant with these factors through daily observation of the birds and learning from veterinary doctors and other farmers.
In poultry farming, the large number of birds under confinement predisposes them to many diseases and disorders. These diseases and disorders are caused by various microbial agents, parasites, nutrition (lack or excess nutritional elements), toxins and environmental/management factors.
This is further exacerbated by age, breed, immune status, stage of growth and level of production. I did note that you carried out all vaccinations as advised by your veterinarian and that was a step in the right direction. But many farmers are misled to thinking that once their birds have been vaccinated, they can relax.
This is a false illusion. Vaccinations are indeed supposed to protect your birds against specific but not all infections. A farmer still needs to observe biosecurity measures aimed at protecting the birds from contact with disease causing micro-organisms.
Cases of vaccine failure, either due to mode of administration or handling, are many. For instance, some farmers use chlorinated water to reconstitute vaccines. This greatly lowers potency. Since you birds were vaccinated, you may need to do a post evaluation of how this was done and whether there are possibilities that you missed out on some steps.
The ferocity of poultry diseases tend to vary across ages. Old stock is normally immune compared to young ones. That is why old and young birds must never be mixed. Poultry farmers are normally advised to thoroughly disinfect old premises and give it a grace period of about two months before introducing another batch of birds. If this is not observed, the chicks will be prone to diseases before they develop the requisite immunity. But since your stock was attacked between the third and fifth month, this may not be the reason you lost your hens.
Environmental and management factors play a critical role in the development and spread of poultry diseases. Aspects like lighting, sanitation, air quality and ventilation must be taken into consideration when constructing poultry houses. Failure to observe these leads to the development of stress among birds which compromises their immunity. Any opportunistic diseases can easily flare up.
Other factors include the quality of feed and water and their availability when needed by the birds. Idleness among the birds can also lead to development of vices like feather plucking. I doubt that your birds lost their feathers due to idleness as the same clinical signs are observed in parasite infestation, allergies and in cases where birds purely feed on seeds and table foods. Loss of feathers can also occur due to skin inflammation or in case of liver diseases.
Loss of feathers can also be a direct consequence of poor air circulation, humidity and imbalance in light and dark cycles in birds. The disturbance in the 12/12 light and dark hours may cause a physiological disorder characterised by loss of feathers.
You also mentioned weak joints and subsequent death. While I may not authoritatively pin point why, calcium and phosphorous deficiency may be the cause. Lack of these two minerals in birds is characterised by weak joints and bones (rickets in young birds and osteoporosis in old birds) and poor shell formation for laying birds. Rickets is also caused by lack of Vitamin D.
Calcium is necessary for the functioning of the nervous system and its deficiency results in paralysis and death. Since you didn’t observe any other clinical signs like respiration (breathing) or digestive system problems which are common with infectious diseases in poultry, the most probable cause of your loss might be nutritional.
But this is only tentative and a further diagnosis by a veterinarian will help you narrow down to the exact problem.
In the meantime, please separate the sick birds from the healthy ones. Dispose off dead birds properly and and don’t let outsiders inside your poultry unit. Also, don’t visit other poultry farms and, most importantly, call your nearest vet.