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.
"Terminat Bora Diem, Terminal Auctor opus."