Along the main road (route 202) outside the main Nagasaki station there are many raesonably priced clean and efficient business hotels. (between 5,000 & 6,000 yen for a single). There's the Belleview Hotel which i have stayed in - clean cheap central (3 people shared a room at 4,000 each) - good sized beds and rooms (by Japanese standards). Highly recommended.

Take the tram two stops to Dejima.
www.hotel-belleview.com
For a list of many Nagasaki hotels see:
www.at-nagasaki.jp/foreign/english/about/hotels/

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