It's been a long time since I've seen a raft really used properly. Most quests nowadays involve walking around, solving puzzles, getting items SMetroid style, and then getting back into some kind of plot. The raft really doesn't seem important, not like the ladder anymore. For example, there's concentration on dungeon design, and plot / theme now. You can use tunnels, and lock blocks, to make obstacles to your design. Besides, the raft is only good for special events such as bypassing lava, or maybe for sailing over "null space" in certain quests.
Have you used a raft yet in your quest? Or have you just stopped seeing them lately?