What does have mean in this sentence?
It does not, as a popular myth would have it, convey 50% of the actual message.
This is simply a variation on the expression rumour/word/legend has it that. Here's how the Macmillan Dictionary defines it:
used for showing that you are reporting something that you have heard when you are not sure whether it is really true
Rumour has it that her husband is not the father of the child.
To make it easier to understand, the sentence can be paraphrased as follows:
Contrary to popular (mistaken) belief, it does not convey 50% of the actual message.
What that popular myth is and what exactly does not convey 50% of the actual message are hard to tell without more context, but the idea here is that there is supposedly a popular myth according to which something does not convey 50% of the actual message.