When talking about printing, literature, or anything having to do with medieval and early modern texts, it is easy to overlook something that must not be overlooked: how much of what was once written or printed has now vanished. For practicas, annual astrological prognostic booklets, which were by nature ephemeral, we can assume that many editions have left no surviving copies, but pinning down how many or characterizing the relationship of the known to the unknown is tricky.
One source of evidence are book lists that can be compared to known editions. For practicas in the 1560s, we have two interesting sources in practica compilations, one printed in Frankfurt for the year 1565 (VD16 ZV 29072) and the other printed in Basel for 1569 (VD16 P 4544), both of which claim to reprint all the astrologers who have made prognostications for that year.
The first collection, for 1565, includes sections from the practicas of ten astrologers: Johannes Huldrich Ragor, Nikolaus Neodomus, Johannes Hebenstreit, Andreas Rosa, Christoph Statmion, Sebastian Brelochs, Gregor Fabricius, Nicolaus Winckler, Simon Heuring, and Moritz Steinmetz. Of these, nine are known from printed editions of practicas for 1565; only Ragor's is otherwise unknown. (This is an interesting list of astrologers. Six are well known practica authors, while four are sparsely attested: Ragor [otherwise attested only for 1581], Neodomus [attested only for 1565], Sebastian Brelochs [only attested for 1565 and 1568-69, in contrast to his widely published predecessor Anton Brelochs], and Moritz Steinmetz [only attested for 1565]. But the editor also omits a few astrologers with practicas for 1565, including Valentin Engelhart, Georg Holsthen, and the well-known Joachim Heller.) In comparison, VD16 records 16 practica editions from 12 authors, but lacks Johannes Ragor's.
The second collection, for 1569, includes chapters from eight astrologers: Nicolaus Winckler, Johannes Hebenstreit, Victorinus Schönfeld, Simon Heuring, Valentin Butzlin, Erasmus Reinhold, Sebastian Brelochs, and Hieronymus Wilhelm. Again, half of the authors are well known, while the other four are more obscure (Sebastian Brelochs again, Valentin Butzlin, Erasmus Rehinhold, and Hieronymus Wilhelm). The editor again omitted some well-known astrologers with known practicas for 1569, including Georg Caesius, Andreas Rosa, and Christoph Statmion. The included chapters are drawn from four practicas that are unattested in VD16.
So to sum up: The collection for 1565 tells us that VD16 misses 1 out of 13 authors (7.7%). The collection for 1569 tells us that VD16 misses 4 out of 11 authors (36.4%). For both years, VD16 records 23 editions from 14 authors. The two collections suggest that VD16 misses at least 4 out of 18 authors (22.2%). This isn't an answer to the question of missing editions, but it does give us some interesting core samples to think about.