My (perhaps naive) thoughts on this are - suppose a 16k-packages-in-one-directory solution were just as fast as a 16k-packages-sharded-by-prefix (the CPAN solution), then the former is conceptually simpler and so should be preferred. And the fact that you can mechanically transform one structure to the other means that the filesystem (or git) should be able to transparently do it for you (eg use the sharded approach as a hidden implementation, while the end user sees a flat directory). This seems to be similar to what ext4 does (https://ext4.wiki.kernel.org/index.php/Ext4_Disk_Layout#Hash...).
The obvious question is how would you implement that. You might argue (as you should) that git has closer semantics to a filesystem than version control. But actually implementing this sharding would require git be a kernel module. Hardlinks and softlinks won't save you because they are both still dentries and thus have the same performance pathology. Maybe you could do it with fuse, but what have you gained by making your version control system even more annoying to use?
