I've been doing the same research for my printable SH3 charts and came to the same conclusions - just as we know the "circumference" of SH3 World is 3125km larger than RL.
Shameless chart plug:
http://www.subsim.com/radioroom/showthread.php?t=213987
The world is definitely equiretangular - programmed from the 120km long lat, which makes life easier for navigation in some ways. Also allows for easy RL comparisons with my coord method (which is less relevant with your Real Nav chart in-game of course)
Another shameless plug:
http://www.subsim.com/radioroom/showthread.php?t=209834
Sea state does affect your speed, just watch the dial. If it moves between 6 and 7 kts I've found 6.5 kts is remarkably accurate for dead reckoning. However I suspect the level of time compression affects this. In still trying to break it to try and find out exactly how much it affects your speed more precisely.