I am sorry to hear about the problems with your pet. I am glad she is getting better.
There are several complications that can arise with microchips. This is one but it is uncommon.
As far as the delay in abscess, it may be related to the pneumonia. After microchip placement, there is a small amount of inflammation as the body forms scar tissue around the foreign object. Any area of inflammation and any foreign objects in the body are at a higher risk for infection from circulating bacteria. We always have a small amount of bacteria in our systems, but when there is a serious infection like pneumonia, there may be high amounts of blood borne bacteria. If the bacteria settled at the site of the microchip, then it could have abscessed. Then again, it may have just been a microchip that delayed in abscessing - this can happen sometimes too. Hard to say. Either way, abscessing of microchips occurs but is rare and should not be a reason to avoid microchipping most pets.
Hope that helps.