PlayStation 2 Memory Card is an ordinary mass storage device like any other. Can be used to stores saves, can be used to store any kind of data. This doesn't matter for applications. Data is data, access is on filesystem level.
MCFS, the filesystem used on PS2 Memory Cards (You can use any like i.e FAT32 in MX4SIO devices but PS2 firmware support only MCFS from this storage), like many other FAT like filesystems, using timestamps of file creation and modification. Some games using them as security level preventing from save modifications. This works in a way that inside save is timestamp and game comparing if timestamp inside save is the same as in filesystem. If they will be different, then game refuse to load it. Another issue can be attribute preventing save copying to i.e another memory card. Both problems solving packing saves into containers which keeps all important meta informations from filesystem and of course saves itself. One of such formats is *.psu. So this is why user should archiving saves in *.psu containers, besides other reason like having backup outside PS2 environment (i.e PC, or just pendrive alone).
Other data than PS2 game saves (PSX game saves aren't protected in such way because PS2 doesn't exist in those times ;]) like i.e apps and their resources, You can just copy as files and folders.
