It might be that the E-D did possess some sort of a utility craft for a mission type that never was witnessed in the show. But we saw pleasure yachting of various sorts, and that wasn't it. We saw infiltration missions, and that wasn't it. We saw flying through dangerous environments, and that wasn't it. About the only thing we missed was the ferrying of large numbers of troops (perhaps the Yacht performed an offscreen role of that sort in "Descent"?), or perhaps the establishing of a research or diplomacy outpost. The thing might be a flying barracks (the shape would certainly cater for it) - but why call it a "yacht", then?
It could also be that a dedicated Yacht set would have been expensive to maintain, and due to the infrequent need for it on the show it was easier to just have Picard in a shuttle, of which one was used nearly every other episode.
We also saw limited use of the saucer separation sequence; the first was in the pilot, for which there was the funding to create the sequence. Later, we see it again but it is re-used footage. The sequence in Generations is a film, so more money available. The writers probably had limited in-universe reasons for needing to see a saucer separation at all, so it was ultimately a seldom used occurrence.
It's the same reason a Runabout was used in Timescape
(easy to borrow the set from DS9) but never seen again. Before that, it was never mentioned that the Enterprise-D even HAD a compliment of Runabouts.