Well, if the partition is nearly full, there is a very good chance that you will start getting much higher levels of fragmentation in new files -- there just isn't that much free space, so what is left is probably fragmented. In terms of fragmentation, it's partitions that count, not physical drives. But for a partition that is used as static storage and is defragmented occasionally, it doesn't really matter how full it is.
FAT32 partitions near maximum capacity can start to have other performance issues... NTFS doesn't really suffer from this.