I'm an adult newcomer to the piano and have been taking lessons for about two years. I have a basic question about practicing scales. Other than helping to learn music theory and to improve manual dexterity, in what ways does being able to fluently play scales help as one grows as a pianist. In other words, is there a greater purpose? Are the scales put to use in difficult pieces?

It depends on the composer. Mozart extensively used scales in his compositions. Beethoven used scales somewhat frequently. Chopin, less so. By the time you get into a more modern era, scales are used less, but still, it is important to be able to play your scales.

Of course, Chopin writes plenty of arpeggios, which have great similarities with scale technique...

Tom, you've almost answered your own question, in part. In the sense that they "improve manual dexterity" they serve a greater purpose. Anything that improves dexterity is an asset. And, in addition to Mozart and Beethoven, I think Schubert uses scales quite alot too.

What I've noticed, and this may be in part because I am an adult student, is my scales have improved quite a bit since I started working on arpeggios.

Scales are kinda funny in a way. It takes quite a bit of technique to play a really good scale. It seems like it should be one of the easiest of techniques, but I don't really think this is true and they take lots of practice. At least, that's been my experience.