In most cases ammonia is not ...

In most cases ammonia is not bad in a boiler.  In fact it is used frequently to control the condensate/feedwater pH.  Ammonia in a cooling tower is a little more difficult to determine the impact.  It can act as a nutrient for biological growth and can promote copper corrosion.  That being said, cooling towers do a fairly good job at scrubbing out ammonia as their is a lot of air/water contact (although the pH is typically 7-8.5 while optimal ammonia air scrubbing is at a pH of 10+).  Also ammonia will react with free chlorine in the tower (typically added by way of sodium hypochlorite) to form chloramines which are lower power disinfectants but tend to have a longer life.  You can get rid of ammonia with high levels of free chlorine but this can be a bit difficult and requires a high level of free chlorine.  You can also send the ammoniated water through an air stripping column but you would need to elevate the pH which could be challenging if the water is highly buffered (high alkalinity) and you would have to consider if the scrubber off-gas would need treatment to avoid emitting ammonia.