The Amiga disk format stores 512 bytes per sector, 11 sectors per track (a track is one side of a cylinder), double sided (i. e. 2 tracks per cylinder) with 80 cylinders per disk, which makes 80 * 2 * 11 * 512 = 901120 bytes = 901.12 kB = 880 KiB raw block data.
The IBM-PC format also stores 512 bytes per sector, but only 9 sectors per track (on a Double Density (DD) disk, as opposed to a High Density (HD) disk), also double sided, also 80 cylinders per disk, which yields 80 * 2 * 9 * 512 = 737280 bytes = 737.28 kB = 720 KiB raw block data.
Neither of those formats is able to achieve that nominal amount when you sum the sizes of the files stored on disk. The more obvious reason is that you always need to store metadata such as filenames, dates, subdirectories, etc. as well. The other reason is that on those filesystems file data always occupies a multiple of some unit (a block on Amiga OFS/FFS and a cluster - consisting of multiple blocks - on MS-DOS FAT12) and if the file size doesn't exactly equal that multiple, some bytes of the last block or cluster are wasted where no useful data is stored.
You are right that the Amiga OFS format also stores housekeeping information on each data block (a block that is used for the contents of the file, as opposed to a block that is used for the file metadata or directory data), so only 488 bytes of each 512 byte block can be used for actual file data, while the Amiga FFS (Fast Filesystem) format uses all 512 bytes of a data block for file data and doesn't store redundant housekeeping information there, that's why you can in general put some more data onto FFS disks than on OFS disks (unless no file on the disk is larger than 488 bytes or your disk content consists only of directories and subdirectories, in which case you can store the same amount).
The speed difference when reading a directory likely comes from the vastly different way each filesystem (Amiga OFS/FFS vs. MS-DOS FAT12) stores directory information on the disk:
MS-DOS FAT12 groups several file metadata structures (that include filename, protection bits, change date, first cluster, etc.) into one block while Amiga OFS/FFS has one file metadata block per file (OFS/FFS directory blocks just store a pointer to the first file metadata block and a hash table for quickly finding a file/subdirectory if you access it directly by filename). That means to list a directory and the names of its contained items, you have to load fewer blocks from a FAT12 formatted disk than from an OFS/FFS disk.