During the day, a werewolf has a human form, so it is logical to call him a luphomo. During some nights, a werewolf has a wolf form, so it is logical to call him a homlupo. Are both forms used? Is one used for both cases? Is it correct to call a werewolf homlupo during the day?
When they are in wolf form, they are a homlupo, and when they are in human form, they are a luphomo. To insist on one form over the other could be seen as a kind of diurnal chauvinism—which body shape is the more authentic?
If you are talking to a lupulo on the phone, and you are not sure of their current shape, you can avoid giving offence by using the word likantropo, or the more inclusive formŝanĝisto and metamorfozulo.
(Note that Zamenhof chose to use lupfantomo in one of the Fabeloj. This is still, more or less, the official word. However, is it possible that he was referring to the ghost of a werewolf, and omitted the -hom- to avoid pedanticism? Who can say?)
Both of these words are used quite a lot, because the card game The Werewolves of Millers Hollow is quite popular at Esperanto events (at least in Europe). The word homlupo is used at youth Esperanto events, while luphomo is used at family Esperanto events. They have precisely the same meaning.
It is hard to say which one of them should be preferred. The only form listed in PIV is lupfantomo, which I have never heard being used in practice, and which has been criticized for being very misleading, as werewolves are not ghosts. I have heard the argument that homlupo is to be prefered, because according to the legend the real nature of the being is its wolf nature. This is the reason why I personally prefer homlupo, though given that I regularly attend family Esperanto events and no longer youth Esperanto events, I now use luphomo more often, just to ensure that I am more readily understood by those used to this word.