I could be mistaken, but I think Project Honeypot is trying to address a different problem - harvested email addresses.
I believe the Honeypot concept that has been discussed on here is referring to creation of a honeypot field on a web form, tempting the bot to fill it in. Many bots will blindly try to submit something into each field, just to make sure that they get all the required fields on their form submission.
By adding a honeypot field, and adding text that instructs humans to leave it blank, a very high percentage of bot submissions will be detected, with few false positives.
Furthermore, you can hide the field from humans, with CSS tricks, as others mentioned. Make it 1 pixel. Make it hidden. etc.
In addition to including specially tagged spam trap addresses, some honey pots also include special HTML forms. Comment spammers are identified by watching what information is posted to these forms."
You're absolutely right that fake fields like that are a good way to catch bots, though, and that making your site unique is a great way to avoid being targeted by mass attacks that go after, say, all MediaWiki sites. Of course that doesn't help when you're big enough to be worth attacking specifically, but it makes things a little harder for the spammers.
I believe the Honeypot concept that has been discussed on here is referring to creation of a honeypot field on a web form, tempting the bot to fill it in. Many bots will blindly try to submit something into each field, just to make sure that they get all the required fields on their form submission.
By adding a honeypot field, and adding text that instructs humans to leave it blank, a very high percentage of bot submissions will be detected, with few false positives.
Furthermore, you can hide the field from humans, with CSS tricks, as others mentioned. Make it 1 pixel. Make it hidden. etc.