I checked, and you are right about there being hardly any direct references to the AutoIt3 project in the sourcecode of AutoHotkey.
However, AutoIt(3) is mentioned many times in the comments. It should be clear, and it is from the Help-file, that portions of the code of AutoHotkey were taken from the AutoIt3 project, credit where credit is due.
So, maybe Chris should indeed make clearer references in the source, especially since this turned out to be such a touchy subject.
The issue here is that the AutoIt3 team got p'ed of by AutoHotkey using it's code, and - in their opinion - not giving enough credit. I feel Chris made up for this in the Help file, where their team is mentioned and credited fully, but you are right about the sourcecode needing more info on this.
The 'old' AutoIt2/Legacy version served as a framework for AutoHotkey in terms of syntax, and parts of the open source from the AutoIt3 project were used for improving AutoHotkey, so, how much more credit can you get?
Since AutoIt3's source is/was (they are changing the licence probably because of this issue) open, and therefore useable, I don't really understand their problem... AutoHotkey is open source too, they can take good code from AutoHotkey and implement it in AutoIt3 in turn...
Both AutoIt and AutoHotkey turned out to be excellent automation utilities, each with their own pro's and con's, most notably AutoHotkey's syntax being easier/less code necessary and it's support for hotkeys/hotstrings, and AutoIt's power (more mature then AutoHotkey), more utilities and 'higher level' programming syntax...
AutoIt3 went thru the 'virus-reporting' stage already, meaning scripters used it to write malicious code. As a consequence, they choose to not have hotkey support (which could be used for keylogging activities), and disabled some other options too. Yesterday my virusscanner gave a warning on the AutoHotkey installer, after updating the signatures, it didn't anymore, but it looks as if the first malicious programs were written with AutoHotkey already too... Hopefully this won't influence AutoHotkeys capabilities.
It depends on what you as user likes, it's not really necessary to start bashing each other's products, since they are both very good...
AutoIt3 however is leaning towards closing their source now, which p'sses off some of their coders (too), since they were under the impression of contributing to an open project. Hopefully the AutoIt3 team will come to senses, and accept that the nature of an open source project is that others can, will and even should use their code.
I have a strong feeling that Chris wants to keep AutoHotkey open, and it would be a true shame if he'd would want to close it somehow someday, but I don't think he wants to do that.