Simple, but speculative answer would be "to make him less likeable".
In the original book Vladimir Harkonnen is just obese. Problem with this is that fat people in the movies usually work as a likeable, clumsy comic reliefs rather than villains and masterminds (which would be even more true for a floating fat guy), but if you cover him with pustules - no one will find him funny anymore.
This also works as a cover for another of his unpleasant trait that has been removed in the movie - he supposed to be a sadistic pedophile*, but displaying it in the movie would give it a much more strict than "PG" rating.
The in-universe reason for his less-than-pleasant look (with pustules or not) is explained in the prequel,
Revered Mother Gaius Helen Mohiam blackmails him into being a father for her child - unfortunately the baby is born deformed and Gaius smothers it in the crib. She asks baron for his "service" again, but this time, he humiliates and rapes her. As a revenge she infects him with a STD that changes his appearance
In the movie he still kills a boy, but his victim is around 16-20, which greatly reduces the evilness of the scene