Call me cynical, but it won't be for long. Both 'Poly and CFC make use of those ads to pay for the bandwidth. You can bet they'll be adding ads up the wazoo.
The whole point of making certain features, such as GOTM, pay-per-use is to raise money without having to have ads. As I understand it, it was felt fair to have a small charge for these features, which are mostly used by the "hardcore" members who would not mind paying a small amount to keep them going. It means a nicer looking site all round.
Of course, everything else remains free, including the downloads. You can continue to download all the files, including mods, scenarios, units, and the rest for free. The File Database will remain basically the same, but Apolyton's files will be slowly added to it over the coming weeks, just as ours were when it was first put up. That means that pretty much all user-created Civ content will be available in a single place, without modders having to check both CFC and Apolyton for that elusive unit. I think the new site will be a real improvement, with the strengths of both of its parents.
I don't really understand much about the timing, but it's basically down to the mundane fact that server bills are paid at the start of each month, so it officially begins today. There was some talk that lots of people would think it a joke because of 1 April. In fact I think they may even have deliberately made the big announcement today so that people would wonder if it's a joke, and that would create some publicity when it turned out not to be, but I don't really know.
As for OT, I don't actually know if the new site will even have one. That might not have been decided yet - there are good arguments both ways. Probably.