My client have created a script in php+mysql that saves images directly in the database and every images has url like this: www.example.com/image.php?id=421
In your
Is there a good reason for storing them in the DB? There can be some valid reasons to do this. I am assuming these are client images not the images needed to display the site itself (i.e. background images, things inside img tags).
As for rebuilding the site. It would likely improve performance, but at a 1000 hits a day it may not be worth the time it would take. assuming site performance was acceptable and it did not incur extra hosting fees etc. I would be inclined to leave it until I was redesigning the site.