Hi Claire,
are you sure they have removed all of his lymph nodes (armpit? throat?) or did you just mean they have removed the lymph nodes in his pelvis?
Assuming it is the lymph nodes near his prostate that have been removed, there are a number of possible explanations. Some surgeons remove the lymphs routinely for all men having the RP (surgical removal of the prostate) while others will remove just one or two for checking. Sometimes the surgeon can see during the op that the lymphs have some cancer in them and they decide to remove them while they are in there.
Dad should be able to ask someone on the ward to explain the reason, if he hadn't been told beforehand that it was planned to happen.