Killzone Trilogy had you put the disc in and it downloaded it to your harddrive for free when you hit the button for Killzone 1. I haven't hit the Bioshock button yet, so I don't know for sure, but the same type of disc button appears as in Killzone.
The original Bioshock is technically on the disc but it has to be downloaded and installed onto your PS3 to actually be played. This 12gb file is downloaded directly from the disc, instead of through the PSN. I just did so yesterday without any troubles other than the loss of that much of my hard drive space.