I had the same question after installing modRana (a map application). After downloading a few of maps, Windows explorer said size 800 KB, size on disk 4.5 MB. Ouch!

My solution was simple: copy everything to the PC, reformat from Windows using the smallest allocation unit size available, copy everything back.

I kept the format at FAT32 but changed the cluster size from default 64 KB to 8 KB (the smallest Windows let me) and my map overhead dropped from 4.5 MB to 1.2 MB. That's a number I can live with. After copying everything back to the phone, I also noticed that my free space increased from about 5.5 GB before to about 7.5 GB after the reformat.

Needless to say, the N900 can still access the partition happily