Which one? There are a bunch of Ys games on GOG; most published by XSEED, the latest (and the upcoming one) published by NISA. Some companies are just not very sale-friendly, or they have certain games in their catalog that they feel aren't "ready" for sales at a certain time.
Since Lacrimosa of Dana has its own subforum, I'm assuming you're referring to the XSEED-published ones. I didn't keep up with the sale all that much, to be honest, so I can't say for sure which games were on sale or not, but anyway, that's probably up to XSEED, I doubt anyone in this place will be able to give you a satisfactory answer, since XSEED people don't tend to hang around GOG forums all that much (if at all). As for GOG, I'm betting they'd put everything they sell on sale, if they could, and they're probably under hundreds of NDAs with each and every publisher they have a deal with, so they really can't disclose much, on their end.