Computational Attacks on Abbreviated Text

[Torsten]

Wouldn't that also imply that the scribe was 'thinking sounds' while writing? That he somehow assigned sounds to the glyphs?

The usage of a special character alone only implies that the scribe was knowing this character.
To demonstrate that a character was used because of its meaning it would be necessary to demonstrate a pattern for its usage. For instance if you can demonstrate that words with an apostrophe are used after or before words with a rare or unique feature this would demonstrate that the scribe was using the apostrophe since it belongs to this place. 
Unfortunately it is only possible to demonstrate that characters where used beside other characters or are preferred for a special place within a word, paragraph or line. For instance the [y] is often used beside [d] and at the beginning or end of words. But patterns for relations between words are hard to find for the VMS beside the fact that words where used near to similar looking words. One possible reason for this observation is that the scribe was thinking on something lese then sounds during writing.