It's an Italian film. It wasn't shown in the USA until late 1955, so I doubt it was projected in 3D here originally. IMDB's technical specs mentions the system as "3-D (Tridimensionale Christiani)".
Someone claims to have a trade article saying the idea of making it in 3D was abandoned. I saw the film when it was first released and as a young child I found it mind-boggling and never forgot that cyclops. It wasn't In 3D. The German DVD with the two versions is very good.
I'll take a look at Tim Lucas' Bava book to see if there's any mention about 3D.
EDIT: cruised thru the small section on Ulysses, no mention of 3D. Of course, it isn't a full focus and Bava's participation is deduced, so it's not a primary focus in the book.