When we boarded the ship NCL took everyone's passports. Before arriving in Egypt everyone had to pick up their passports, and they were already stamoed with the Egypt tourist visa.
There was no mention made of cost, though I had heard the visas were $20 PP. If they are going to bill it to our shipboard accounts there was no mention made of it.
After returning to the ship from Egypt, we had to again hand in our passports, and were told we'll get them back before arriving in Turkey... and again, with the visa stamps in them. Once again, no mention made of costs.