It depends on the circumstance. Some boolean operations are very concise without any cleanup. Others can require a boatload. Typically, if I use them, it will be one of the last things I do to an object. For example, look at a disc brake...booleans are great for creating the small holes and any grooves. Things like that become more difficult to do manually creating circular holes because of all the splitting/cutting you have to do. Like anything, there are more ways to model something, all with pros and cons. Do what's most efficient in getting the job done.