I have been a few times during the past six years. The only boat still operating there, that I have been on, is the Don Questo. It is 30 m sturdy steel ship, a former fishing trawler built in the late 60's, that used to sail the nordic sea. She was turned into a naval research vessel in the 80's and then into a commercial diving ship in the late 90's by an italian scuba club. She's italian owned and the captain is very flexible and offers true unlimited diving. It's no problem doing 3-4 dives a day, but you need to have the group with you on that. DQ also has a small hyperbaric chamber on board - the only one in Sudan as far as I know. I know Lorenzo (skipper) had plans for Nitrox, but I don't know if it has been actualized yet. It's not luxurious, but the food is very nice, the dive fascilities well suited for the fanatic diver and the captain is flexible and easy to deal with.
I've been on the Royal Emperor to Brothers etc. when she was owned by Yasser El Moaffer and sailed in Egypt. It's a purpose built dive vessel. There's no boat in Port Sudan that can compare to her when it comes to comfort. Don't know the new owners or in what 'spirit' the ship is run now, but it's probably a very good alternative and the only one delivering NITROX in Sudan. Check what type of tenders they have today, as it is crucial for the diving in Sudan where dingy rides can be very long and sometimes in rough water, especially in the south.
To my knowledge, the only way to dive Sudan from Egypt today, is by joining a transition trip in the fall. Most boats go to Egypt or Europe over summer for service and/or charters in the med. Then you fly back from Port Sudan. There are no boats doing regular trips from Egypt to Sudan like back in the days. I did a 17-day cruise once going from Marsa Ghaleb to Port Sudan and then back to Egypt again. But even with that many days it was hard work for the crew with a lot of night sailing. It would be interesting if a ship like the Royal Emperor would start doing Hurghada-Port Sudan and you were able to joing the ship in either Hurghada and then fly home from Port Sudan or vice verse. A two week itinerary eith Brothers-Deadalus-Elphinstone-Rocky Island/Zabargad-Elba Reef, Pfeiffer Reef, Angarosh/Mesharifa/Abington/Merlo-Shab Sudei/Ble Belt-Sha'ab Rumi-Sanganeb-Umbrea. That would be something.
BTW. I don't want to play political adviser and to go or not to go, but I can give some facts. Sudan is a very big country, the biggest in Africa. I have been there several times when the civil war raged in the south and also when the troubles in Darfour started and never noticed anything, felt unsafe or uncomfortable. You should always check the current political conditions however with your foreign affairs department. It is an unstable part of the world.
cheers
Christian