Over a thousand messages in your Inbox? Local or otherwise, the Inbox is a special folder and shouldn't be used as a dumping ground. I don't care how busy you are. Even though good clients and servers can handle this, I recommend an email reorg.
If you don't, this might cause undue stress if you're maxing out your n900 with music, browsing and what not. You could still experience problems and frustration resulting from slowdown and/or scarce resources such as memory. Clean it up and be happier.