Depending on your meaning, I wouldn't say they were common, but they were perhaps not unknown. There are two basic categories of item you'd be looking at: the prop book and the deliberate forgery.

The prop book would be a book created just for the appearance of the thing, the kind of thing that is seen today in Hollywood movies whenever Ancient Tome (1, Bound In Human Skin) is called for, and in the 16th century might have seen the light of day in plays like Christopher Marlowe's The Tragical History of the Life and Death of Doctor Faustus (1592) - although note that there is no evidence for, or surviving examples of, prop books from these early performances. Another use of a prop book might have been to give the right air to the shop of an alchemist or herbalist - although again, historical examples of such are slight; the earliest use of a book as a prop I'm aware of is from the early 19th century, and that was actually a copy of Barrett's The Magus - for details, see Owen Davies' Grimoires: A History of Magic Books 136.

The deliberate forgeries were actually relatively common in the medieval period - especially among monks, who were generally literate and had access to both records and scribing materials - the most famous of which is probably the Donation of Constantine, but any number of papal bulls and other documents were forged for one purpose or another - you might like to look at The making of medieval forgeries : false documents in fifteenth-century England, which has three great case studies in it of just that sort of thing; and that doesn't include the innumerable texts which were attributed to a different author or provenance (very common for many occult and alchemical texts).

For the Voynich Manuscript in particular however, neither explanation is exactly satisfying. If it's a prop book, it's a very elaborate one, being written out entirely by hand by one or more scribes, on vellum, with illustrations, using an artificial alphabet. If it's a forgery, you can't read it, so what's the point? Unless, of course, the very point is that you can't read it; William Voynich suggested that someone sold it to Rudolph II of Bavaria which means that it could have been forged as a deliberately unreadable herbal just to make a buck...but I'm not aware of any other books like that from that era.