Downloading songs from external hard dirve

Try Dupin or Dupin Lite. Dupin is $15 from the developer's site, and Dupin Lite is $8 from the Mac App Store. I recently purchased the full version and used it to delete duplicates from a 57,000 song library. It did a very good job. It's filtering mechanism is highly customizable. It is not super fast, but it ran through my library in less than a day.

To specifically deal with your issue, you can set the rules to keep the file with the shorter filename. This will get rid of the commonly found "whatever the song name 1.mp3" file, while keeping the "whatever the song name.mp3" version.

Also, dougscripts.com should be your first stop for any iTunes maintenance scripts. I have found the following scripts especially useful in cleaning up large iTunes Libraries:
Artist - Name Corrector
Super Remove Dead Tracks
Search-Replace Tag Text v2.0
Track Parser
Remove n Characters From Front or Back

If you enable iTunes Match, your entire library (up to 25.000) songs will be synced with your iCloud. So all your songs are in the iCloud. You can add a device to the iCloud and by so, all your music on the new device will be synced onto the new device. That's how iTunes Match works.

If you computer/hard drive gets stolen, you buy a new one and authorize it with you iCloud, it will sync once again on your new device.

So yes, you'll be able to download all your music stored in your iCloud onto new device.

As a matter of fact, even when the original device lost it's files, the songs are still stored in iCloud.

But be aware, the limit on devices is set on 10. So make sure you haven't add 10 devices already!

EDIT:
Proof of this is on the iTunes Match-page