Hi Cobra,
The boxed version and the download version are two separate ways of ordering. No, if you opt for the boxed version you are not automatically entitled to a download link. It is because two versions of SSE cannot have the same License key.
I have a boxed version and in "My Account" in shipsim.com, I do not see any reference to my boxed version. It will only list license keys of the downloaded versions purchased separately.
Regards
vin_sun