I have a 6am departure from the Istanbul airport. Do I need to be at the airport to go through security the usual three hours or does it take longer?
If you are flying back to the U.S., it will take much longer. Everyone has to go through security just to enter the airport plus there will be PP checks while in line to get your ticket. Next, you go through security to enter the gate area, and at the gate you will also be vetted 1 or 2 more times. If you are flying to the EU, am pretty sure you will have to go through the same process, however, going to non-EU or domestically, doubt you'd have the verifications above, other than at entry into the airport and screening to enter the gate area.
I just came back from Istanbul yesterday. I had my boarding pass printed ahead of time and no luggage to check. The first line was just a luggage scan right inside the entrance - it was pretty short and took about 5 minutes. I did not need to go to the airline counter, which would have been Turkish Airlines, since I had my boarding pass. The main wait was at the passport control line - that took about 25-30 minutes. After that, I was able to head to the gate, which was another 7-10 minute walk. A third screening happened right at the gate by some private security company (likely hired for all US flights) - that took no time at all.
My flight was at 1:40pm and I arrived at the airport a bit later than I wanted to (a little past 12:00pm), but I still made the boarding with maybe 5 or so minutes to spare (I was in the first boarding group and it started one hour ahead, at 12:40). I don't think you need 3 hours, but certainly 2-2.5 would give you a more relaxing check-in. If you aren't checking bags and have a boarding pass ready to go, that's ideal. It's hard to guess how long the airline counter line will take, some are easy and some are crazy crowded - I've arrived way to early on another occasion and the counter wasn't even open until 2 hours before the flight. PM me if you have any other questions. Of course, it's also best to stay as close to the airport as possible. I loved my hotel - let me know if you need ideas.