Hands and arms are not an issue in many business headshots as they are always cropped out of the photo. However, it's a good idea to get your photographer to take wider views as well as the cropped version. These wider views offer a little more flexibility when laying out future marketing material.
In many business portrait photos people often cross their arms. This can work well if the subject is entirely relaxed in front of the camera. However, alternatives to the 'crossed arm' shot should be found as it can sometimes seem defensive and non approachable.
An 'action' shot is usually the answer to this dilemma. You can hold a pen, a file, a clipboard or a bunch of papers. Technological gadgets such as phones, lap tops, tablets can help out but be aware that they may quickly date a photograph. Remember that people will relax more in front of a camera when they are actively doing something connected with their work environment.