So my wife is due Oct. 26th, which is going to prevent me from participating in the league for, at a minimum, one week. For all I know, she might go into labor tonight. As a result, I may end up with a Win % that doesn't take into account the trading and deck improvements people make for those two weeks. So what does everyone thing should happen here?

if you are selfish enough to have a child during the Nerdery League Magic League, than I feel strongly you need to deal with the consequences.
Or, maybe you just play so many games before you leave that at the end of it only Eric and Bill have more than you do and we just go with that win %? I would guess that you are on track for that second option, even if you were out the next week and a half...

I guess the problem is that decks will improve over the next two weeks (new boosters + more deck experience). If I'm not participating during that time, I'll have an unfair Win %.

Maybe no one cares, but I want to make sure in advance.

Same thing happens if someone's project goes into crazy deadline mode or for whatever other reason doesn't have time to play anymore. It happens, and I see this as just for fun.