It may just be a display error since the timer has disappeared. Have you tried doing a forced refresh, or even just press the travel button and see if the hyper and sublight options are there? If they are you should just be able to set a course on the minimap which should refresh the main screen.
Travel still appears to be completing normally, although the issue with timers not displaying is known and is being worked on. You should still exit hyper when you are supposed to; you may just be incorrect about the exact ETA you had.
Downtime is "stopping the clock" on travel too, so if your ETA was 12 hours but the server was down for any of that time, the clock wasn't running so you were basically standing still while the server was down. I started a 12 hour flight myself just as the server went down for a better part of the day. The entire flight ended up being nearly 24 hours by the time the server went down, came back up, etc.
Never try to teach a Gamorrrean to sing; it wastes your time and it annoys the Gamorrean.
I posted it on bugs, they made a temp fix...least I can see the ETA now. It is in the position area, the ETA is a little longer than it should have been, due to server downtime I suppose, but at least i got out of HS. ;)