Let's say you want to do a PhD on American reactions to the Soviet collapse. Unfortunately, for a substantial amount of archive material you will need a security clearance.
As historians, how would you handle referencing and bibliographies as well as various other issues that come with handling classified material?
So I have a long post here about accessing sources without a clearance.
With a clearance presents very different issues. I've never had (or wanted!) a clearance, so I can't speak to those authoritatively. But I do know official historians (and have read accounts by them) of how this has worked.
Historians do sometimes get security clearances. Obviously this has to be done for what the security-granting agency thinks is a Very Good Reason. So these tend to be official historians (e.g. historians who work for the government) or historians who have some kind of very close connection to the government agency they are dealing with, and the study presumably is one the government has to be convincible they care about. (So these tend, from a historiographic perspective, to be pretty conservative, "just the facts, maam" sorts of productions, and not Derridean analyses whose worth, if there is any, is hard to convey to a bureaucrat.)
Two things to keep in mind. First: A clearance does not get you everything. You still have to establish "need to know." So there are still limitations on what access there is in many cases.
Second: the condition of getting a clearance (in the US anyway) is that you sign what is essentially a contract that says, if you are going to publish on any topic that might possibly be informed by your secret info, you have to run it by the declassification people first. And they — not you — decide what must be deleted before the final output is published in an unclassified form. (If the final output is meant only for classified eyes, presumably they determine the classification level of it.)
So I have read several histories of nuclear weapons that were written with classified sources but then made releasable to the public. In some cases the authors are explicit about some of the changes they had to make, e.g., in one case, the author had to avoid all discussions of a specific warhead, and instead had to create a sort of "composite character" warhead that was based on real examples but was so blurred in the specifics that nobody could learn any secret information from it. (That is a weird case, to be sure — they even came up with a fake code-name for the composite warhead.)
In one case I know of, an official historian was not at all able to publish on a topic because it embarrassed some current officials. The historian in question thought there was zero security risk. But the office of classification wouldn't approve the release, because someone higher than them told them not to. This is totally against the rules and probably technically against the law, but these kinds of abuses are not punished in the United States classification system. I have chatted with said historian a bit; he told me that as an official historian there are real incentives to work on older topics where everybody is dead and nobody has any "skin in the game," and that to do otherwise is to invite such headaches.
(In the US, there are massive punishments for releasing too much, and essentially nothing for releasing too little. So you can see how the incentives would shape the results.)
In another case, a historian found that one book was entirely put on hold by one tyrannical military official unless he promised that his next book would be about a subject the official wanted written about. The historian acquiesced, and that was that. But it gives you some hint of the power dynamic. (I have talked about this incident a bit here.)
What about non-official historians? I know a weapons scientist from the 1950s who wrote a set of memoirs, in essence. In fact, I helped him make sure there was an unclassified source for every controversial, potentially-questionable statement he made about weapons work — so he could claim to the government that even if he was informed by his (now many-decades old) access to classified information, it was all information that was unclassified anyway.
Nix, said the government, and told him to delete a bunch anyway. But he is in his 80s so he told them to take a hike and published it anyway. Technically that put him in legal jeopardy, but since prosecuting octogenarians is a bad look, and the government trying to censor stuff tends to bring even more attention to it (once is already out there), nothing to my knowledge has come of it in terms of bad consequences. (You can read more about this incident here.) One can imagine under different circumstances there might be different results.
As for referencing, these histories tend to reference reports, etc., and indicate their classification level. Usually report titles are themselves not classified. Their report numbers never are. So you can reference, "Report on the Top Secret Thing (TS), Report 43231," or something like that. Is that useful for other scholars? A bit — if I have a reference like that, I can FOIA it, and maybe see some of it. Even without that possibility, it's nice to know there's some kind of citation — maybe someday it'll be released. Is it as good as an open citation? No. Does it entirely fit the bill for scholarly practice and transparency of sources? No. Is that part of the tradeoff of using classified sources? Yes.
As I said, I have no interest in using actually-classified sources. For me, there is no joy of knowing without also being able to talk about it. It's the reason I'd never try to get a clearance — and the reason that no government agency with any sense would give me one!
You might be interested in this Monday Methods post that covers this topic in extensive detail from /u/restricteddata, who deals with precisely this issue professionally: https://www.reddit.com/r/AskHistorians/comments/7hgwoi/monday_methods_using_secret_sources/