Aqueducts are able to produce several orders of magnitude more water per day than a ground well, or even a collection of many ground wells. The larger cities of the Roman empire in the first century CE had tens or hundreds of thousands of people in dense urban environments. No amount of ground wells could serve such populations. At the height of the system, the aqueducts serving the city of Rome carried over a million cubic meters of water to the city per day.

...and as to your second question: many of the aqueducts had castellae meant to be staffed with soldiers for their defense. Also, except for Hannibal's rampage through Italy, the Romans did not really have many adversaries capable of besieging the city. This was less true in the provinces in some periods, but in general the Romans did not have to deal with many sieges. I'm not an expert on how poisoned water supplies work, but the sheer volume of water traveling through an aqueduct must have made poisoning them effectively difficult. Partially destroying an aqueduct was a possibility, but they were built to last and, again, not many enemy forces had the time to seriously damage one beyond repair.