It is hard to know for sure, since recurrent pneumonia is common in premature infants as a consequence of bronchopulmonary dysplasia (BPD). It is also common for infants who have had respiratory syntactical virus (RSV) to go on to develop asthma. While possible, it is unlikely that your son’s issues, especially his upper respiratory issues, have been due to allergies. On the other hand, were excessive mucus production, which you refer to as "the drainage from everything”, the combination of premature lungs associated with impaired mucus clearance could present as pneumonia. It sounds like he is getting good, comprehensive care, resulting in your son doing very well, and that is terrific.
I should add he still has a diagnosis of BPD also... (broncho pulmonary dysplasia), and asthma...