hi,
Dunno if it can help, but :
a directory is no more than a file storing filename associated with the node number (the filesystem only use number to store file and the name are only here for our poor humans

)
So if you have had a monstruous number of files in the directory /var/log, the size of the /var/log file 'yes, I mean file' ! ) becomes great also.
And the fact that you have suppressed the file don't reduce the size of the 'directory file'. Instead, the inode number is set to 0 (that's the general approach, i didn't works a lot with the ext3fs)
In old Unix system, there was only one way to change that :
mkdir /var/log2
mv /var/log/* /var/log2
rmdir (or rm -r) /var/log
mv /var/log2 /var/log
unfortunately, you cannot do that in runlevel 7 (to much open files)
But Linux comes with so many wonderful tools, maybe is somewhere one to 'pack' your directory ?
HTH,