Actively mislead can certainly suggest intent; its range of meaning is visible in the definition of actively (Oxford English Dictionary, "actively, adv.," def. 1).
- By one's own action; voluntarily, deliberately; spontaneously; positively. Opposed to passively.
Deliberately suggests intent, and similarly actively commonly suggests intent. (Someone often intends to do what they do.) Many of the examples in the question fit that usage, e.g.,
Might they be actively misleading readers?
That said, actively is opposed to passively, not innocently. It is possible for someone to bring a situation about by one's own action without intending to bring that situation about, as through ignorance or neglect. For example, from your examples:
The name bin_digits is actively misleading: it does not contain the binary digits.
The name bin_digits cannot intend to mislead. Nor can we know if the person who named the file intended to mislead. In any case, the name misleads actively, that is, the name contains incorrect information that leads people to an incorrect conclusion.
Less trivially, in this example, the writer may make a choice that happens to actively mislead readers, but it isn't clear that the writer intended to deceive; they were likely sloppy in formatting, but the formatting had what the speaker considers to be an active role in misleading them:
If you just write some consecutive paragraphs of text and put a bullet point in front of every one of them, you are actively misleading me, because your layout tells me I can skip around, while the content should be read in order.
As a matter of precise style, I'm not happy with actively mislead. The usual sense is strong or even accusatory. However, if even file names and data can actively mislead, then deliberative action or intent isn't the sole way the phrase can be used. Actively can act almost like explicitly or even very, an intensifier for how misled someone felt they were.