Some letters aren't letters

[Emma May Smith]

Linguistically, this could represent a 'stop'. I don't know if there are any known examples where these are written. However, they would make sense in running text and might not be needed in front of single words. Also the next character would have to be a vowel. (Looking forward to Emma's comment on this).

Alternatively, they could be similar to the Greek 'spiritus'. (Vague memories of my one year of classical Greek).
These also only occur with vowels.

I don't have a comment on your q as stop suggestion, but the idea below it is very much my current thinking. Rough breathing in Greek is (well, was) a remnant of heta which represented the /h/ phoneme. That sound occurred in a very curious environment: 1) it was always before vowels (ignore rough breathing on rho, as it has a different origin) and 2) always at the beginning of words.

The non-occurrence of q at the beginning of labels could be due to the proceeding word. We know that not only does q have to appear before o, but two-thirds of the time it is after y (which is likely also to be a vowel). The sound may well depend on a very precise conditioning environment for it to be readily apparent to the writer and therefore worthy of representation.

The character y is interesting in yet another way.
It is very frequent, and it seems to behave almost normally.

However, when one makes a list of the vocabulary of Voynichese words, one find that more than one third of all words ends with a y.

I just cannot see how any natural language would behave in this way.

In some languages all or almost all words end in a vowel, and the Voynich text may only have two clear vowels in o and y. I'm not convinced that vowels are fully differentiated, even though they are fully marked. The two vowel characters could simply represent a fundamental feature (such as front and back, high and low, rounded and unrounded) or even length. It could be that multisyllable words often end in short vowels due to prosodic considerations.

Here's an example of a herbal page with labels:

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The labels, consisting of three Greek letters, are in fact numbers.
The labels we see in the Voynich MS could be verbosely encoded numbers.

Greek letters were regularly used as numbers (as you know). But this is not verbose encoding, rather it is a separate use of the same characters, switching from phonemic to morphographic. I think that the use of Voynich characters as numbers can be mostly ruled out, for various reasons. The labels themselves are too well-structured to be numerals, anyway.