Water injections will work on most crosslinked phases like what Restek produces, so damage from water is not the main concern, especially with a low injection volume or high split ratio.
What you will need to watch out for with those columns will be peak distortion due to the fact you are injecting highly polar solvent onto a highly non-polar stationary phase. If the oven temperature is below 100C, then the water can condense on the column. If the column is polar, then you get a nice smooth film of water on the initial portion of the column which can actually enhance the chromatography. If the column is non-polar, the water will tend to form droplets or an uneven film since it will tend to bead instead of making a film.(think water on a well waxed car finish) This can distort your peaks and lead to poor chromatographic performance.
To make a column work with a dissimilar solvent, you can add a guard column/retention gap to the head of the column that has a proper polarity deactivation layer on it to let the solvent film form on the cool column. Once the temperature ramp begins, it will again evaporate and pass through the column in a much better shaped peak. The same works for the analyte of interest, it can help to sharpen the peak with the proper guard column attached. For the ammonia you may want to add a base deactivated guard column to help it form a better peak on the non-polar column.