In 0.50 there is a known issue with wells no longer being functional. However, this has actually had quite a positive effect on the survival aspect of the game. For the first time I have actually encountered people who approached me because they were severely dehydrated (and starving!). It created a much more interesting player encounter dynamic, since so many people were being forced to try and survive.
In all my play time I can probably only remember 2 or 3 times that my character was ever thirsty (the vast majority of the time I am healing or healthy), and I had never met anyone that really needed food or water before. I believe that keeping some degree of the unusable well situation would greatly enhance the that aspect of the survival component of the game. Wells could be randomly set on server restart to either broken or working.
In addition to that, an interesting balance for the wells is that they are a bit of risky thing to use, this could also be enhanced by introducing the need for priming (pumping for a minute or so) if the well has not been used for 'x' amount of time.