I also purchased and downloaded my initial copy of SH3 directly from the Ubi store. That was almost a year and a half ago, and it came fully patched to v1.4. So I'm pretty sure gwol's version is already updated as well.
IIRC correctly it was the same or cheaper than buying the disc from Amazon (which I did anyway, eventually, just to have one on hand).
@ gwol: Welcome aboard!
You may also be able to tell what version you have just by checking the Properties of the SH3.exe file in your game folder. Find the file (should be in the main folder of the game installation: usually Program Files\Ubisoft\Silent Hunter III if you let it install in the default location) and right-click on it, choose Properties. Under one of the tabs in that Properties box there is usually a version number.
As Steve said above, you can download GWX3 from Jimbuna's FF page here:
http://www.filefront.com/user/JimbunaGWX2/
You will need all of the GWX3 .bin files plus the GWX3 .exe file. Save them all to the same place on your hard drive. If the .exe filename is missing the .exe extension after the download completes, right-click on the file name and add it. Then double (left) click on it to open it and it should proceed with the installation.
It must be installed over a clean, unmodded installation of SH3 v1.4, so you may need to uninstall and reinstall the game itself first before adding GWX3.
Have fun and sink 'em all!