That's actually what Spotlight Search is for. Many people including myself probably forget about this feature.
Yeah, the way I use my folders is not by subject, but importance. I have the apps I use most out of folders on the home screen, with one or two folders for other apps I use pretty often, but not every day. My second page is for overflow apps that I like to know where they are, but don't use them constantly. Those are not in folders. On the third page, I have all the rest of my apps in lots of folders, almost completely unorganized, just so I can limit my pages to three for cleanliness reasons. Anything I need that is not on page one or two, I ALWAYS find via Spotlight Search. Super easy.
But, what works for me might not work for anyone else. It's how I like it, and the app limit for folders has never bothered me.