Ammonia is alkaline, but the organic acids are produced by various bacteria and fungi which break down all sorts of waste products in the tank. pH tends to drop over time also because the process of converting ammonia to nitrate uses up bicarbonate (KH), which causes a drop in KH and a corresponding drop in pH. A tank therefore which is seeing pH considerably lower than tapwater inclines one to suspect that KH is very low; this is bad for a couple of reasons:
1. Bacteria can't convert ammonia if there's no bicarbonate;
2. The same bacteria can't work at very low pH;
And, of course, if there's nothing to stop the crash, a very low pH where acidosis can occur may be the end result.
It's also very dangerous to cure. You might imagine that you can just raise the KH (bicarb does the job) and all will be well. But often the fish, to the aquarist's surprise, drop dead as soon as he does this. This is because of the inhibited bacteria. If they are inhibited by lack of bicarbonate and low pH, then ammonium builds up - this is the non-toxic NH4+ form, which predominates in acid environments (plenty of H+, you see, to combine with NH3). As soon as the bicarb is added, the pH rises, but this causes the NH4+ to convert to NH3 - toxic ammonia. And this can kill fish fast. A rise of 1 pH point effectively makes the NH3/NH4+ ten times as toxic, because as has been observed, the pH scale is logarithmic. A single point is a ten fold decrease in the concentration of H+ available, which leads to a ten fold increase in the amount of ammonia in the toxic NH3 form. pH drops therefore shouldn't be treated by raising the KH until the NH3/NH4+ level has been checked (fortunately, aquarium test kits give ammonia as total NH3 + NH4+; the disadvantage of this is that you need to cross-reference with pH to find the level of NH3. This doesn't matter much as we always want it to be 0 anyway).
This phenomenon is also part of OTS, because it's caused by insufficient water changes to maintain a steady KH (main means of replenishing bicarbonate is from water changes). Another indicator is high nitrate, because the same water changes are also the means of removing nitrate, but in a planted tank this indicator may not be seen.
Clearly this tank hasn't got to this point yet, because ammonia is reading 0 and nitrate isn't high. But I'd want the GH and KH compared to tap to see if it's heading in that direction, and if there is a difference which is contributing to his current problems.
Whew! How can a simple chemical like H2O have such complex chemistry? Actually, it doesn't, it's the bleedin' things which dissolve in it!