Could be they have done it like that, but I suspect the Navionics card
reader also works like some sort of a hardware authentication key
(dongle) for the RayTech Planner software.

I rather doubt Rayplanner's dependent on the Navionics device. Mainly since
it's capable of speaking with an E-series over ethernet. But then I suppose
that's the ultimate dongle, eh?

The only thing the software will read from and write to is a card
reader and not just any card reader, the software must identify the
card reader as a Navionics card reader.

Mmmm, not sure about that. It won't read the Navionics charts unless
they're in a Navionics reader. But it'll import/export to other media just
fine, including other CF cards.

It's an efficient way to protect the software because you need a
special piece of hardware, the Navionics card reader, to use it.

True, the combined burden of making cards that physically won't work in
regular readers and the requiring that reader appear with a special USB ID
hwid is certainly a dastardly way to screw your customers. I mean, yeesh,
we've already spent $500 to buy they're eff'ing charts and they still want
to treat us like thieves? Jackasess.