The plays as we have them in the First Folio are the best versions, those that were written and produced for the Court or the Inns of Court. By 1623, there wasn’t nearly the danger that public audiences would guess the connection between those characters based on important figures of the 1580s and ’90s, for most of them were long dead and, without newspapers or memoires, public memories were short (no danger, that is, so long as the true author’s name wasn’t involved).

The problem for the publishers of the First Folio lay not with the general public, but with the aristocracy. However short the public memory, the aristocracy is based on the length of their memories, which means that to this day they are concerned for the reputations of their ancestors. That acquiring the rights to the plays and the agreement of those concerned required years of negotiation would be obvious to anyone who has followed the troubles that attend the posthumous publication of the collected works of any author whose family has acquired control of his or her papers.

In a small community like the 16th-century writing establishment, there was no way that a writer with a known style could get away with using a phony name. (If I should publish a biography of the Earl of Oxford under a phony name, one completely unfamiliar to those who read such books, how long do you think that it would take my audience to guess who actually wrote it?) However, the use of a real person meant that suspicions could stop with a simple denial. John Aubrey has left us an anecdote about William that says that “He was not a company keeper; lived in Shoreditch; wouldn’t be debauched, and, if invited to, writ he was in pain.” Or there was another option, to could pick a front who lived too far from London to be a problem, someone like Edmund Spenser for instance. On the page “Who was R.B.,” do a find for Essex, and you’ll find an interesting sidelight on the use of initials, and the risks that authors and publishers ran when too many people knew the truth.

In any case, your question is important and points to what must have been a genuine concern. I believe that some of the things that were attributed to Marlowe following his death were actually by Oxford, who had them published as by Marlowe because they were too sexy to risk attributing to someone alive ( by then, of course, Marlowe was past questioning). I also think it’s pretty clear that Bacon got very reckless in the early ’90s with Spenser’s name on his Mother Hubberd and again later with Nashe and the Isle of Dogs. Too bad we’ve completely lost track of the real Thomas Nashe. It sure would be interesting to know what happened to him.