Yes, all timers in the Emu are "real time" timers. Harvesters continue to harvest, Factories will keep producing, and all maintenance will keep deducting. If a resource times out while the server is down, then you will find the amount you would have received deposited into your hopper and the harvester will be turned off, just as if the resource timed out while you were offline normally. The only difference is that resources, instead of being replaced soon after they despawn, will be replaced (if needed) in the process of bringing the server back up.