I don't see the connection in having buses mixed into the departures board @ union train station. It seems about as relevant as mixing in streetcar departure times, or heck, even porter departure times. I think you should know already if it's a train or bus no? Isn't the station in another building? I can't imagine there's a big use-case for people walking to union station, realizing they need a bus, then going to the bus station. It's not like trains and buses leave frequently enough that you can just show up to take the next available one, taking the GO is a planned trip (unless on Lakeshore). If a scheduled train is being replaced by a bus, they can have a CANCELLED / BUS status, and the passenger can look at the bus board instead.
I think having a separate screen for the bus schedule makes perfect sense though, for those that need to determine if they need to run or walk to the bus station. Putting in VIA departures makes much more sense (and honestly ,getting rid of the separate VIA concourse and modernizing it like Bay and York). Maybe the way this can be done is have a mix of "Union Train Station" departure boards, and agency specific "Metrolinx Live Schedule" / "VIA Live Schedule" boards, which can have more info.
What is the reason for not having late night service on these lines anyway? Is it just a budget thing because of the small number of people travelling, or is it that the tracks are used by the freight trains during these times?