If they were to boot out everyone who hadn't logged on 45 days prior to the patch, then we'd see a ton of open lots. With the email warning system they're doing, we probably will get a few people coming back to the game just to protect their plots, but I'd guess the majority of those obviously empty houses are still going to be reclaimed after the 45 days.

As far as Ishgard housing goes, unless they change the way Ishgard access works, it's going to be pretty hard for Free Companies to even consider getting houses there, as it precludes any new players who don't have level 50 classes from even seeing the FC house until they level up and finish the 2.X storyline.