I think the two dots may have been used to distinguish iotas from other letters involving vertical strokes, but don’t expect consistency. Probably the same reason for the single dot over i in Roman minuscule/lower case.
https://en.wikipedia.org/wiki/Greek_minuscule
The 9th century was a period of the renewal of learning and scholarship after the Iconoclasts. The oldest Greek mss. of classical authors (apart from papyri) date from this period. Some of these manuscripts were very carefully copied by scholars, not by ignorant monks, as is commonly thought, and often they were corrected by one or more editors. However, if you spend much more time trying to read Greek minuscule, you will soon need a seeing-eye dog.
The Cod. Bodl. MS E.D. Clarke 39, usually designated by the siglum B, was written in 895 by one Ioannes Calligraphus, at the direction of Arethas of Caesarea, one of the leading intellectuals of the 10th century Greek world. The new Oxford Plato edition of the First Tetralogy describes Ioannes as scriba satis diligens, a rather diligent scribe, although according to Burnet it contains various errors, particularly of omission, and much of it was damaged by humidity, with the damaged passages filled in by a later hand, so that what Ioannes wrote is illegible in many places.
I probably should have waited for mwh to comment, since he will be so much more knowledgeable than I about this, as well as about everything else.
This book is essential reading:
https://www.amazon.com/Scribes-Scholars-Guide-Transmission-Literature/dp/0199686335/ref=sr_1_1?ie=UTF8&qid=1540003464&sr=8-1&keywords=wilson+and+reynolds+scribes+and+scholars
Maybe this will help you. I think this is still available in reprint. It’s outdated to be sure, but I think still useful:
https://archive.org/details/greeklatin00thomuoft/page/n3