I am also trying to do this, but nobody else knew. I think I found the solution, I just don't have it working yet. If you want to try yourself, you will need to know PHP and mod_rewrite. Cydia sends the UDID along with a few more special headers in $_SERVER:
[HTTP_USER_AGENT] => Telesphoreo APT-HTTP/1.0.592
[HTTP_X_FIRMWARE] => 4.0.1
[HTTP_X_MACHINE] => iPhone3,1
[HTTP_X_UNIQUE_ID] => xxxxxxxx
You could use mod rewrite and send Release to Release.php, same with Packages and Packages.gz. Then check if $_SERVER['HTTP_X_UNIQUE_ID'] is in a list of approved device ids before including the requested information. I'm not sure how well this will work, but I am going to try it. I am having troubles with Cydia finding changes in repos, but I'm sure this could be fixed by sending a few modified date headers.