In the end, pen names are ultimately in favor of either protecting your identity or serving as an amusing alternative identity that you can find relation in. They are often times self given as a safety net should you work on projects that you feel quite uncertain about or would not want to officially be known for. If you worry that values you find poor will reflect on you and your family with your work, then it would certainly be a good idea to utilize a different alias for that.
Concerning payments, if it involves companies and legalities of monetary concern, you can stipulate in your written agreement ( if any ) that you wish to utilize an alternative name on the project while retaining the payment notice for your official. I myself have done this before and it works even greater in speed without all the write ups. This however falls through if you are receiving payments from something that is not an organization or group because at that point the cat is out of the bag with who you disclose that information to since there are no binding agreements for the information you reveal.
At this point I pretty much just don't care who knows my official name. I often work with three names being Shane_frost, Callmedoc, and Doc-Diventia. Only because I just enjoy the ring to them. If you have something to protect, protect it. If not, go nuts.