I'd say it's possible that some Dwemer may have traveled forward through time. The connection between Dwemer and the Elder Scrolls is only really brought up in Skyrim, and the Dwemer in that province were of a different clan to those in Morrowind, presumably with different ideology and practices too. Skyrim also introduces the idea that the Elder Scrolls may be used to travel through time. It is implied in the Song of Pelinal from TES IV that Pelinal Whitestrake also traveled through time, although through totally different methods - he was effectively an incarnation of Akatosh himself. TESO also involves time travel, I think.
However, the event known as the "disappearance of the Dwemer" took place during the event of Red Mountain, and really has nothing to do with the Elder Scrolls. The artifact that those Dwemer were using was the Heart of Lorkhan, along with the Numidium that they created. This was later reconstructed and used by Tiber Septim to conquer the provinces, and appears in the resolution of TES II: Daggerfall's plot. The Dwemer in Morrowind seemed to be much more focused on achieving a sort of enlightenment than manipulating time. All we know now is that they are not here, so I suppose transporting them into a future is at least a possible outcome, although it seems less related to the events of Morrowind (which if you're interested in the Dwemer, you really should look into - Skyrim and Oblivion don't contain every book from it, and some are vital to understanding this mystery).
The "another plane of existence" thing is to me just terminology. I don't necessarily mean that they went to an Oblivion plane or anything like that. More that their existence is now on some totally different level unknown to us. There is the theory that they became "animunculi", meaning "small souls" - these are not the robots you see in their ruins, but rather fragmented spirits that effectively power those automatons. This ties into the theory of "subgradience", which essentially states that through the course of creation, spiritual forces become more distinct and fragmented in a process of indivuation and self-knowledge. First there were the forces of Anu and Padomay, which gave rise to gods, which gave rise to Nirn and the mortals within it, which may in turn become something different. Supposedly, the Dwemer sought to reach the last subgradient, an end-point to this process, where all souls would be perfect and eternal, safe from the confusion of existence. Nirvana, effectively.