What is the relationship of Gingetsu and Ran? Captor and captive? Protector and charge? Lover and beloved? Maybe at one time or another, all of these things, and like so many of CLAMP's relationships, it's ambiguous at best. But although there may be other interpretations, and I don't deny that the manga leaves their story with an open end, for me their interaction leads to this conclusion. They may or may not ever have become lovers as Ran grew, but they are certainly in love.
Clover is not presented in order. The start of this relationship is not shown until Book Four, but when it's focused on, every moment is closely followed and examined. By the end of this volume, it is clear that Ran and Gingetsu are together not only because of circumstances and needs, but because they want to be. They come to admire each other and earnestly need to be together. Gingetsu wants to help Ran and keep him where he is so much that he is willing to implant a suicide device within himself. And when he confirms this with Ran, Ran responds that he wants to stay where he is. It may be tentative, but a connection has sprung up between them.
Chronologically speaking, the next time we see these characters is when Kazuhiko, Gingetsu's second in command, introduces his lover Oruha to Ran (book Three). At this point, Ran looks to be somewhere in his teens- remembering that it's actually only been a year or less, and that he's undergoing rapid aging outside the cage. It's clear from the way Kazuhiko talks throughout he doesn't know exactly why the two are living together (his first comment on meeting Ran was 'You're into kids now?'), but what's interesting is the way Gingetsu and Ran react to his comments. They both seem completely at ease with him, each other, and all his talk about their supposed affair. To me, this seems to hint that they've come to a conclusion about how they feel for each other, and whatever it is they're comfortable with it.
This also holds true in the main storyline, which is set a definite two years after Ran first moves in with Gingetsu (he now looks like he's somewhere in his twenties.) Although Kazuhiko still doesn't know the circumstances that tie Gingetsu and Ran together, he is their close friend, so it's probably safe to assume that he's observed the way they live.
It's no wonder that Kazuhiko isn't sure what's going on between the two. For one thing, up until the start of the main story, he knows nothing about the Clover program. He doesn't know that Ran is older than he appears, that Gingetsu was himself subjected to a Clover's childhood, or how little time the both of them may have. We, the readers, know better.