I went to Japan on Feb. 2014, I am allergic to shellfish. I did a lot of research. First thing, it is illegal to bring an epi-pen to Japan and almost impossible to get a special permit to get them in the country. I got the printed card and also a pandora charm that said I was allergic to shellfish. I carried with me Benadryl everywhere. Server at restaurants and even at McDonals will go a mile extra to make sure you don’t eat anything that is not safe for you. I learn how to say in Japanese that I have an allergy and I could die besides carrying and showing them the card so they took it pretty seriously.
I starve some times because most places will not have anything safe to eat. McDonalds cook its shrimp burgers near the regular ones, so the only safe thing on the menu are their french fries. At the Japanese burger chain MOS you can have burgers but not french fries as they fry shrimp on the same oil. Vegetarian food is your best bet! Curry houses are fine, and any Japanese zen Shojin ryori cuisine should be safe. Be careful with desserts I love dango but you should not eat the salty/soy ones as they can contain dashi (dashi has always seafood), the sweet flavors are fine. Beware of steak houses, I had a reaction after having lunch at one (I could controlled it with 2 Benadryl) they cook the meat and shellfish in the same surfaces and even if you ask them to be extra careful as my guide did, it just didn’t worked. Foods you should not eat are: miso soup,fried food, okonomiyaki, about street foods (yakitori can have shellfish on the sauce, little round things some times are baby octopus which I am sure taste delicious.)
Go to a convenience store or a supermarket and get basic sandwich meat, cheese and regular bread (don’t get fancy with ingredients you don’t know it can cost you) and prepare some sandwiches to take with you in case you can’t find anything to eat. I mostly survive with dessert, sake and beer. I am planning to go this year again and I am glad now I know I should try to look for vegetarian restaurants instead of trying to find something to eat and being frustrated because I can’t have anything. Also planing to bring some of those lunch tuna snacks and other stuff to make sure I am not eating dessert for dinner.That said, people in Japan are super polite and accommodating. I really love Japan and I will try my best to make sure I stay safe and away from shellfish.
Please do tons of research about the area you are going to, contact your hotel if is small to make them aware, tell your guides, look in happycow.com for vegetarian restaurants in the area you’ll be staying and do the same at trip advisor.