Yes, if an attraction is not popular, reducing the scope and making the experience less impressive is certain to bring the crowds in! Stage shows generally get a pass for theme. Technically, the theater is in Dinoland, but it's kinda sorta its own thing. Having Festival of the Lion King as the only attraction in an Adirondack-themed land doesn't seem to keep the people away, btw.
If Nemo is not pulling the crowds, I think it's because nobody is presold on seeing a "Finding Nemo: The Musical" the way they are with Beauty & the Beast or Aladdin or even Lion King. I'd bet there is a good chunk of people who see that there's a "Finding Nemo: The Musical" and think, "Finding Nemo? What songs do I remember from Finding Nemo? Ehh, pass." While it's a laudable technical achievement to take a movie without any songs and turn it into a musical, maybe theme parks are not the right venue for that. On Broadway, it works because there is a whole cottage industry of Broadway criticism that people are used to accessing and usually set out to see a specific show. Theme parks are different. Broadway is haute cuisine; theme parks are comfort food.