Hi, EK usually sends out such emails in case either Business class is not full at all or in case economy is overbooked. Since you're not flying a lot with EK, I suppose you don't have a status card and as such should hope on an opup. This would be your cheapest way to fly business.
If you do decide to upgrade after check-in it may indeed be more expensive. If the $1000 is within your financial means, I'd take it for such a long flight (especially if it is an A380), but it depends on how much you value space and attention...
I'm not sure if this amount changes from your destination, but I paid once $500 for a 5-hour flight, so I guess you're getting a decent proposal (non negotiable of course)