Chloramine is a far superior form of water treatment than free Chlorine. As Weezard has stated, plants cannot absorb Chloramine, nor does it interfere with growth (this is debatable. Some people claim that Chloramine does in fact harm plants, especially aquatic plants, so I'm not convinced its harmless, just less so than free Chlorine). Free Chlorine can block absorption of specific nutrients (as can Sodium). Another advantage of Chloramine is that it is much less likely to form carcinogenic compounds such as Carbon Tetrachloride, than Chlorine, which can do so freely. But it's not perfect. It is not as effective at sanitizing, and if present in too high amounts, can cause respiratory problems. Also there is some evidence that Chloramine can increase uptake of Lead in animals. I'd rather not have chemicals added to municipal drinking water. On the other hand I don't want amoebic dysentery either. Chloramine is a better alternative to Chlorine. I checked and my tap water has Chloramine, so I no longer will let my water sit. Some municipalities still use Chlorine so you have to check. Chloramine is readily absorbed by activated charcoal, so if you really want to remove it, passing it through charcoal should work.

As for anaerobic microbes, well, that's yet another reason to make sure your conditions don't suffocate the roots. Overwatering and poor drainage are probably bigger indoor horticultural problems than nutrient issues, but never get as much attention.