I'm not sure what the official WikiTree policy is. My own practice is to only put Jr. in the "Suffix" data section if the child is so called in the birth record. In the biography, I only use Jr. and Sr. if those terms are in the record I am citing; for example, if a man is called Joseph Brown Sr. in his death record, in the ===Death=== section of the biography I call him that, or if he is called Thomas Smith III in his marriage record, in the ===Marriage=== section I call him that.
It can get somewhat confusing when working with the records of colonial New England (and perhaps other venues) when all the men living in a particular town with the same name were given numbers according to their birthdates, regardless of relationship. In Berwick, Maine, for example, there was an older Nathan Lord, and then Nathan Lords born in 1710, 1718, 1723, and 1724,(one of them the son of the elder Nathan) and they are identified variously in some records as Nathan Lord I, Ii, III, IV, and V.