There might be some secret technology that we're unaware of but as far as we know magnetometers can only be used to detect underwater targets at very short ranges. I highly doubt that they're used on military reconnaissance satellites.
No, a submarine wake can't be detected at any significant depth. That idea has been tried several times and it never worked, not enough signal. I suppose I can't rule out some secret scientific breakthrough but the basic physics involved make it highly unlikely.
