Using an experienced advisor is a good choice. They will make sure all your bases are covered, talk business valuation with you, help you through due diligence, draft the asset purchase agreement, etc. Doesn't sound like you're asking for those details though.
Most 'pitfalls' should be taken care of in due diligence. Due diligence is the process of making sure what he says his business is, is actually what it is. It also helps you verify that anything that could come back to you if not taken care, has been taken care of.
So about employee morale, it really depends on the size of the company and the type of workers. Honestly, your employees shouldn't be affected much. You're bringing in more work and subsequently new employees, no threat means no real worry. Also, their day to day routine won't be disrupted.
For his employees, first why don't you want them all? If his business needs all the employees to run, why couldn't you use them? Typically right before the deal closes, both you and him would gather his employees and tell them what is happening. The owner talks you up and gives his faith in you. You introduce yourself, tell them that they have jobs, expect little changes in their day to day work etc. Usually workers are just happy they still have a job. The uncertainty scares them and truthfully if they are going to be going to a new location that complicates things. Saying you only want half the employees complicates things as well. Because it sounds like there may be a larger disruption than normal, I would take all the employees and expect to lose a few. Most acquisitions I've worked, the employees don't have much disruption and all they know is that ownership has changed. They still have the same desk, compensation, daily routine, etc. Well at least at first anyway. I have a client doing this exact talk today, but make sure to wait until right before the deal is done, you want the change to be immediate. Don't tell them they are being bought and give them a month to think about it, you run the risk of losing employees.