The US Public Health Service does not like fresh eggs They claim that the egg shells cannot be cleaned properly in order to prevent salmonella poisoning. The USPH also insists that fresh eggs must be stored refrigerated (always below 41 degrees F) to avoid spoilage.
In most cases, fresh eggs must be stored apart from other protein items causing storage challenges.
Strangely, most countries on Earth do not even bother to refrigerate fresh eggs and do not seem to have any problems with that - or with salmonella poisoning from fresh eggs.
However, since ships are forced to store them refrigerated, this creates storage challenges.
Too avoid possible salmonella problems, substituting pre-shelled and pasteurized eggs makes the USPH people very happy, resulting in higher USPH inspection scores - which makes Cruisecritics happy.
These pasteurized eggs are also stored frozen, which is easier - and they can be legally stored with other food items.
Most cruise lines use the frozen pasteurized eggs for baking and for scrambled eggs. Fresh eggs are still used in many cases for omelets - unless the ship happens to be in a US port and expects to be inspected by USPH. Then the fresh eggs disappear, and the frozen ones come out.