First, pretty bad idea to think that it could have been cuz they were tampering with an elder scroll. It has been stated over and over that they disappeard the moment when Kagrenac used the tools on the Heart of Lorkhan. No Elder Scroll in the middle.
Besides, i think they're already proven their mastery of the Elder Scrolls with designing a machine capable of reading it (so no Dwarven would have to read it himself and get blinded in the process).
Second, the Quest of the Winterhold College gives a hind of what could have happened to them (i almost covered my face literally when the dude was hiting the gem with Keening lol i was thinking "Its going to explode, we're all going to die! " )
The guy that i dun remember his name (let me check in the uesp), Arniel, dissappears. Whle in his own words, the experiment isnt 100% accurate since a. He doesnt has the Heart of Lorkhan. b. He doesnt knows much about what he has to do or how it works. c. He lacks the other tools
So, if we assume that what happened to him its exactly or very similar to what happened to the Dwarves, jumping all that bout the heart of the god and the other tools (if the quest can jump over the fact that you're not supposed to be able to use Keening with your bare hands, we can jump over lore too

), there is the fact that the player can summon Arniel's Shade after the experiment.
What it is exactly his shade? I dunno. He can move around, but he cant talk, nor has any expression. Its like he is there in image, but not in soul and body,
The thing is that you draw that shade from somewhere to summon it, That is some very useful information, the thing has to be somewhere esle to summon it from there, and that the player has not the ability of summoning anyones else shade but Arniel alone. So, maybe, just maybe, Arniel IS somewhere, and we can summon his image from there.
There is the idea that maybe everything except his shade was left after the experiment, but there is also the idea that he is in another realm from where we can only summon his shade. Like an avatar of his real form (this is possible since many times, powerful beings appeared as avatars in Nirn, sometimes in their "complete form" like Akatosh's avatar, or Nocturnal's avatar, or sometimes in their disembodied forms, like most of the Daedric Princes apparitions in their shrines).
Probably since he wasnt anywhere close to being a powerful entity in Nirn, nor in other realm, the only expression of himself he can commit to the player once he/seh summons him its his image (or maybe it is a limitation of the player's summoning abilities). Maybe he is in a place so far, so unknown, not Atherius, not Oblivion, that you can only summon his shade from there (that would explain that no matter how skilled is the player in conjuration, you are only able to summon a shade).
So my guess is that the Dwarves, as Arniel, are somewhere. Not in Nirn, not in Oblivion, not in Atherius, but somewhere. Maybe between all those realms, maybe in another one.
Probably no one can make contact with them cuz all of the Conjuration school revolves around summoning from Oblivion. No one, for example, can summon an Aedra from Atherius. So we could assume that the act of summoning differs when taking in account other realms rather than oblivion, maybe summoning its different for each realm, something like a completely different school of magic that, while doesn't differs in purpose (making contact or summoning beings from other realms), it differs in its ways and means to do so.
Thats my "theory" ;P