That's a good question and there's no general answer to it.
It's a fight between performance and security. When you got a last gen computer, Intels Core or AMDs Phenom, you wont notice any real performance loss.
Generally speaking, I don't see much sense in having your itunes library encrypted but I would like to have the
system drive as hidden partition.
There are major advantages to it, although even if there are no known issues with it, I wouldn't suggest that solution to everyone, as you at least should know the very basics of a computer. Like how to change bios settings, install windows, create bootable disks and such.
If you're too lazy to set that up (will take you an hour, no work ever after that), you're better off if you at least encrypt your programs (so many security leaks in some of them), your personal folders (outlook saves it's data there-) and anything else that might contain sensitive data.
I would suggest to encrypt your windows and program partitions, but leave your storage as it is.