Quick answer - Yes, always. Here's why...
Almost all modern automotive paint systems are designed to use clear coat. All major vehicle manufactures use it, all body shops use it, and any reputable touch up company should too.
The clear coat is what offers your color the protection it needs. It will have UV and chemical resistance as well as other protective qualities. Because colors nowadays are designed with clear coat in mind, a lot of them will be formulated to use the clear to bring out the desired finish and the true color.
Without going into much detail, the clear is needed to achieve the proper finish and it will be the protection your paint needs to last for years. Do not skip this step - always use clear coat.