APT 1.6 enables compressed indexes by default.
Bugs
Use of internal apt files is tracked by the apt-internals tag. This is mostly packages accessing /var/lib/apt/lists/directly.
https://bugs.debian.org/cgi-bin/pkgreport.cgi?users=deity@lists.debian.org;tag=apt-internals
https://bugs.launchpad.net/ubuntu/+bugs?field.tag=apt-internals
Performance regressions and other bugs with compressed indexes are tagged compressed-indexes.
https://bugs.debian.org/cgi-bin/pkgreport.cgi?users=deity@lists.debian.org;tag=compressed-indexes
https://bugs.launchpad.net/ubuntu/+bugs?field.tag=compressed-indexes
Reporting bugs
For the Debian bug tracker, add
User: deity@lists.debian.org Usertags: apt-internals
(or compressed-indexes, or both headers)
For Launchpad, just add the respective tag to the tags field.