Having a full encrypted system solves all of those issues. If not, at least an encrypted home (such as what Debian provides with their default installation).
I've tried the both of them and generally I found dm-crypt + LUKS to be superior. The problem of e-cryptfs (which I believe what Debian uses for home directory -- at least Ubuntu uses) limit usable file name length because of the way things are encrypted. While it's not often the case I would exhaust its length limitation, but if I do, it's bit frustrating...