The problem with pre-modern crime statistics is they have to be based on reports. For this reason, when modern criminologists look at crime statistics deep into the historical past, they generally prefer to rely on murder. Why? Bodies tend to be recorded. Here’s a typical example of that sort of research: “Long-term historical trends in violent crime” from 2003. Ted Gurr’s 1981 classic “Historical trends in violent crime: A critical review of the evidence”, I think similarly on focuses on homocide. The one exception I’m aware of (and this isn’t exactly my field) is Guido Ruggiero’s 1980 Violence in Early Renaissance Venice. I don’t think he calculates an overall “rape rate”, but it was roughly equal to the number of homocides (while being concentrated in the female half of the population). One suspects, however, there was underreporting.

The period you propose is hard for a couple reasons: 1) given the social stigma of being raped, women (and men) who were raped would have many reasons not to report it. Being known to have been raped might severely damage one’s marriage prospects. With limited forensic techniques, unless there were trustworthy (presumably male) witnesses, the accusations had a decent likelihood of devolving into a he said/she said at best. Some single women, to avoid this social stigma, ended up marrying their rapists. It’s a tale as old as time. It’s mentioned in the Bible (the Rape of Dinah) and in some countries, like Turkey, it’s still possible for rapists to avoid jail time by marrying their victims.

Second, there wasn’t necessarily anyone to report to, or anyone maintaining these statistics. London’s public police force is often recognized as the first in the world, and was only founded in 1829. There simply weren’t criminal investigators in the way we have today, which I expect would mean (among many other things) that familial sexual assault of child would be grossly under reported.

The thing is, “cross-national homicide rates are also significantly correlated with levels of robbery, assault, and sexual violence” in periods for which have good data, which lets researchers assume that the rate of sexual was likely similularly correlated with then homocide rate in earlier periods. Hence, to understate rates of sexual assault, social scientists generally look to homocide rates as a rough proxy. These comparisons aren’t perfect, but they’re really the best I’ve personally seen.