Can I leave an unused conductor when running wire for an extractor fan?
The best thing to do with an unused wire is to mark it 'unused' at each end and then wire it into the earth connection at both ends. That way there won't be any loose wire which could possibly touch a connection and become live accidentally, and if it did the protective device would open.

Lighting circuits are usually 5A fuses or 6A MCBs. 

Running 3+e to the fan (live, switched live, neutral, earth) allows you to use a fan with a built-in over-run timer. 

If running 3+e you may need a triple pole isolator for the fan, eg

https://www.tlc-direct.co.uk/Products/MKK4859.html