In a post on the Bungie forums, engineer Mat Noguchi explains that the slower loading after a full HDD install is a direct result of how the game was designed to use the HDD in the first place. "When Halo 3 runs, if a HDD is present, we copy maps from the DVD to the utility partition on the HDD," says Noguchi. "And as a result, it means that even if Halo 3 is already installed to the HDD, it will still copy maps to the utility partition."
The problem: copying from the HDD to the HDD is slow. "Ultimately this is because for the HDD, you read and write through the same mechanism, i.e., the hard drive read/write head, and those reads and writes cannot occur simultaneously through a single mechanism," Noguchi explains. The moral of this story: don't install Halo 3 to the HDD and you'll be much, much happier.
Bungie has no plans to issue a post-NXE launch fix because, as Naguchi writes, "The risks of doing that and the resources required has to be carefully considered against what could really be a rather insignificant change to the player experience."