There's plenty of bacteria going around in any marine tank, and that bacteria is quite prolific if you kill a little of it. (in other words, no you don't have to worry about UV hurting your nitrifying bacteria population, it won't cause an ammonia problem)
What do you hope to accomplish by running UV? As MrTuskfish said, UV is not an effective way to deal with ick and other common parisites in most situations. UV will help with water clarity and will be very effective in battling (rare) green water blooms, but it doesn't do much else in most home reef applications.