You've covered a couple of topic areas:
1. Safety of water.
As with any destination in the Honduras, on Roatan it is wise to drink only bottled water. I do get periodic reports of divers developing GI distress, occasionally serious, at both resorts & restaurants.
For example, CoCoView had a major problem for a while, bad enough that it was written up in Undercurrent
http://www.undercurrent.org/ several times within the past 6 month, although it apparently has quieted down now.
This thread from our board archives goes into detail on the prevention & treatment of traveler's diarrhea---->
http://www.scubaboard.com/showthread.php?s=&threadid=12608&highlight=travelers+diarrhea
2. Malaria.
There indeed is malaria on Roatan, and current CDC risk areas include, "Honduras: Rural areas only, including all areas (including resort areas) on Roatán and other Bay Islands." Luckily, it is not prevalent, and most visitors do not take malaria prophylaxis.
However, because it does exist, and because of the ubiquitous no see ums (sand fleas), one will at the least want to take preventative measures against being bitten.
The last reply in this thread from our board archives goes into great detail on such preventive measures---->
http://www.scubaboard.com/showthread.php?s=&threadid=9382&highlight=permethrin
Hope that you found this helpful.
DocVikingo