I've hesitated a bit with answering this, as ultimately any answer I can give is a bit anecdotal. I've certainly never heard of historians facing much in the way of personal danger, and if they did I would suspect it was due more to whatever political identities and/or roles they had rather than their scholarship per se. I've certainly heard stories about difficulties in access to sources, but mostly of a bureaucratic nature - many relevant materials relating to the Civil War were naturally held in military archives (indeed, they often still are), and obtaining the correct permissions to access them could be a nightmare, and the archivists themselves (often members of the military) could be less than helpful depending on your project. They are still somewhat bewildering to navigate at times, though I would say that the main military archive for SCW material (Archivo General Militar, Avila) is now one of the friendliest archives I ever worked in. Even when it was under less collegial management, however, I don't think Spain was exceptionally difficult terrain for researchers in this sense - many European states were considerably less open about official archive access in this period, requiring much more in the way of credentials and permissions for researchers, and restricting access to politically sensitive collections.

Beyond anecdote, there are reasons why we might expect historians to face relatively few dangers of this kind. The first is that the Pact of Forgetting often gets interpreted a bit too literally - there was no nationwide consensus to just never mention or discuss the past or to stop writing history, but rather a decision not to embark on an wholesale effort to litigate the past and to judicially or politically punish those who were part of the former regime. Yet while this meant that there was less of a formal, national-level conversation, it would be a mistake to assume that this meant that the past was forgotten, histories stopped getting written and that memory wasn't fostered and preserved at other levels. Though there has certainly been an intensification of work to preserve historical memory of the civil war and the Franco regime in the 21st century, and it's become much more of a live national issue in contemporary Spain, there was never a time when these discussions ceased entirely.

The effect of this on the historical profession was therefore less of a chilling effect that prevented new investigations, and more the preservation of an artificial historiographical divide. Francoist historians like Ricardo de la Cierva could more or less continue exactly what they had been doing under the regime (ie veering wildly between triumphalist and apologist fantasies), and those historians who had framed their history writing as implicitly or explicitly anti-regime could continue on writing in opposition to these narratives. The result was post-1975 history still being written along quite partisan lines, even well into the 1990s and 2000s after the end of the Cold War robbed the underlying ideological conflict of the remainder of its contemporary relevance beyond Spain. It's taken a long time for more methodologically innovative work that isn't beholden to partisan narratives and subjects to emerge in modern Spanish history writing, and even longer for a new generation of more conservative historiography to escape the Francoist legacy and start doing more rigorous, credible work that isn't just reaffirming the regime's narratives (though some would certainly still argue that these historians have updated rather than jettisoned these older narratives). This, to be clear, is my subjective assessment of the way historiography has evolved - I've no doubt that others would disagree!