It's an interesting question, and I'm glad to see that you are still using the wonderful Wallace and Gromit to teach you English.
To answer your question - no, we don't consider cups, storms or any other inanimate objects as 'women'. The only 'things' that traditionally took feminine pronouns were boats and ships. The custom has always been to give sailing vessels women's names, and to refer to them as ''she ' and 'her', but they weren't actually seen as women - just creations that deserve affection and respect, like real women do ;).
So why do Hagrid and Wallace use feminine pronouns for these objects? For a start, it's worth bearing in mind that both these characters have been given strong local accents and use slightly old-fashioned dialect forms from the regions they originate from (Lancashire in the case of Wallace and England's West Country in the case of Hagrid). This allows the writers more licence for their characters to use non-standard English.
Wallace says 'Fill 'er up, lad' because 'Fill it up', as a command, might sound rude and abrupt. 'Fill 'er up, lad' , by contrast, sounds warm, friendly and informal.
In the West Country dialect of England it's not unusual to use 'human' pronouns for inanimate objects, even today, so this is why it sound natural for Hagrid to refer to the storm as 'she'. According it semi-human status also indicates a certain level of fear and respect for the storm. After all, major weather systems like hurricanes have always been given people's names, haven't they? Hurricane Katrina, and so on. Until recently, they were always given women's names, too..