As a rule communities of bacteria present in soil will change their community structure based on which nutrients are available to them. If there is excess nitrogen being applied you will likely see increases in nitrifying and denitrifying species of bacteria. If you get increases in these species which use nitrogen, increases in metabolism could potentially decrease the air to media ratio in a pot situation.
The main disadvantage to using salt based fertilizers (inorganics) is not so much the bacterial communities being affected, but rather the fungal communities (mycorhizae). These fungi which associate with roots do not "like" the salts used in inorganic fertilizers. If you look at inoculating agents with mycorhizae in them often state that they should not be used with fertilizers high in salts.
Each person must find what nutrients fit their growing conditions and augment their own "fertilizer formula" to match this. For example I grow my plants in an indoor environment, under T 5 lights, at a constant 72 degrees and 45-55% humidity. I add more magnesium and sulfur (Epsom salts) to balance out the application of potassium muriate and offset the lower light in an indoor situation. I also do not want my plants growing huge too fast, so I have decreased the amount of nitrogen in my mix. I also inoculate all my new plants with mycorhizae and a few bacillus species and so far have had good results using this route. This however may not work for everyone, I would conduct your own experiments and report back what you find