Thing about Thursday though is that it's Day Zero; the con has not actually started yet, they're still getting everything set up, the dealers are arriving and setting up their booths, attendees from out of town are most likely driving/flying in, and so on. Putting on any panels on Thursday would be effectively turning a four day con into a five day con, requiring the out of town folks to take an extra day off and arrive on Wednesday if they want to make sure that they won't miss something they want to attend that gets scheduled for Thursday.
Same sort of thing on Friday morning, too; things are still being set up, people are still arriving, and Friday is probably the day that registration is hit the hardest. On the assumption that people are arriving/waiting in reg line (even though Fanime has most thoroughly kicked Linecon's ass,) it makes sense to start the main events later Friday morning/afternoon so that as many attendees as possible will be able to participate.
Plus, and I'm sure any of the Fanime staff can correct me on this, I doubt they are allowed to start setting up everything until Thursday morning most years, and maaaybe Wednesday afternoon if there isn't an event in the con center or the hotels right before them. (That was an issue I believe two years ago? An event right before Fanime was slow in packing up and clearing out, delaying Fanime staff from even starting setup.) For a con this size, they are going to have an enormous amount of equipment to assemble, get into place, wired, tested and debugged. Setup for something on that scale almost never goes completely without a hitch, meaning there's any number of Things That Can (and Will) Go Wrong. Opening any actual convention activities Thursday erases that time cushion they have to iron out the inevitable bugs.