I am a travel agent and I have been on several cruise lines over the years. It is my experience that all of the cruise lines have a wide variety of menu choices available in the dining rooms and other restaurants, such as the buffet, etc. There have always been vegetarian selections on the menu and you can certainly make special requests for your meals, too. There are also low-fat, sugar-free desserts. I've found a lot of variety and flexibility in the menus to suit every need.
Your travel agent doesn't need to make a special note of it - you need to make a special request on the airlines, but not on cruise ships for the more common special meal requests, such as vegetarian or low-sugar. The dining steward will be able to give you more information and details on the preparation of the meals.
Have a great cruise!
Cruising Co., Etc.