When I went to the RLD in Dec 2014, it was amazing. There were girls in windows everywhere. I'm now visiting again but the place seems dead. I went last night at about 9pm and I saw one window girl on the entire RLD canal. Is this government shutdown thing really going all the way through with it?

9pm is still quite early. According to the girls themselves it is now incredibly difficult to find a free window to work in at night so don't worry when you see it like that. I agree though that at times it seems dead. A couple of times I've walked around La Vie en Rose when it should be full but every curtain has been closed with no music or sound whatsoever. I can't explain these things but an hour later everything is busy again.
The partial shutdown is due to continue over the coming years. It will only affect windows in the Sexy Land area (Tromp, Dolleb etc). Everywhere else will remain exactly the same though there's a good chance that several windows in and around Boomsteeg will re-open after nearly 10 years closed. These closures have been planned for nearly 10 years and the plan has actually improved a bit with less windows due to close than originally intended.
We are also seeing work done at Utrecht to re-open that RLD so I am pretty positive about the future of RLDs in Holland.

What are the pickings like during the daytime? What are the September crowds like? Probably the worst thing about the dam. The fucking crowds.

This is why I go during the early spring and fall. Just as many girls around, half as many tourists. Much less crowded, much more relaxing. I'm an introvert with social anxiety. I would never go during the summer.

What would you say the best time to visit La Vie En Rose is so that all the windows are full?

It wasn't dead last night. I find that 10pm is the time that most of the girls have arrived at work. It's also the time with the most tourists. Good business may or may not have started by then. I usually figure that sometime between 11pm and 1am is the time for the best selections of girls and less crowded straats. Most of the girls work until 2 or 3am or even later. I don't know anything about the daytime schedule. I am a night prowler.