There are no piracy in sudanese waters that I've heard of, but some has been reported in Yemeni waters as well as in Somali waters (which is really not the Red Sea, but Gulf of Aden). Border lines with Eritrea are however sensitive areas and best avoided.
When you say "most trips are operated from the Red Sea area" I'm not quite sure what you mean, but these days all liveaboards for sudanese waters operates out of Port Sudan. Some years ago it was possible to go from Egypt and then motor/dive your way down to Port Sudan and then back up to Egypt again. I have done this once. Unfortunatelly this is no longer possible, unless you catch a transition trip with one of the italian yachts either going to Sudan from the med. or when they leave the Sudan for the med.
Allthogh it is possible to go for one week, I'd strongly reccomend you to go for 14 days since the start up cost for a Sudanese dive safari is more expensive than one in Egypt. To get to Port Sudan you fly from Cairo with Sudan Air, leaves every saturday night.
Cost Cairo-Port Sudan RT: app. US$400.
Then you have to pay tourist tax and dive permission.
Cost app. US$ 100 for one week, US$ 180 for two weeks.
Cost for liveaboard app. 700-800 US$ / week.
+flight to Cairo
Roumors say that there will be a new flight travelling from Milan or Rome, via Saana (Yemen) and then to Port Sudan.
You also need a tourist visa for Sudan, which can be a bit of a hassle to get hold of. This you will need help with from either a travel agent or directly from the boats agent in Port Sudan.
Please note that most liveaboards only offer two dives a day and one night dive a week. To avoid this, better gather a group of divers and charter a ship and negotiate / write a contract BEFORE you pay. I have done this a couple of times with different ships and have now found a favourite called the Don Questo. As far as I'm concerned this ship offers superior service compared to other yachts in Port Sudan. Some of them doesn't even look sea worthy. Other boats to reccomend: Felicidad II and SY Elegante.
Conditions can be spartan, however the diving is first class.
The season for Sudan is september-may, since there are no boats with Air Condition. I have been in Sudan in july once (on AC ship) and it was very hot. The water was more than 30 C=sharks went deep. But we had alot of manta rays. Best season for sharks is the winter/spring. Best season for mantas is fall (september/october).
Can't direct you to any specific tour operators (I always deal directly with the ships owners) but there are quite some in Italy and also one in Germany (Sprirosub) and Diving World in London who arrange trips to Sudan. But please note that the travel agency is of less importance. It is the ship and its captain and crew that will make it a good or a bad trip.
good luck
Christian