Nite-Owl in Watchmen didn't have the eye make up on, but he wore goggles most of the time. He also had quite a few moments where he took his mask off, so it would have looked awkward to do the switchover, like Keaton's famous mask removal at the end of BR.
But aye, the mask does not look as good when he has the goggles off, the superhero look is lessened I would say, he looks far more ordinary, rather than larger than life, as he should.
The eye make up helps give them that otherworldy superhero look, that sets them apart from the ordinary person.
It looks awkward in Batman Returns when Keaton makes that switchover, but they just about get away with it as it is a very quick moment.
But in that moment, you can ascertain for yourself whether it's a good idea or not, and I would say that Keaton kooks better in the mask with the eye make up on.
What it simply is is an attempt to replicate the look of the artwork in the books, so they have to draw a wee bit in to get there, lol. Superheroes in masks don't really look human in comic books, they have blank eyes most of the time, the make up helps give us an effect onscreen like that.
edit: Even apart from the obvious fact that it would be nigh on impossible to design a comfortable mask that sat exactly round your eyeballs.
As SH said, it makes the eyes pop out, better than any mask would.
Man, when i used to play in a band, i wore make up just like that round my eyes, a. cause i had deep set eyes, it suited me, and it made me look better onstage, and b. cause i wanted to be and look like a superhero. I never thought about the fact they did it in the movies, I was just copying Syd Barrett who wore eye make up onstage, lol.