Being a startup site, where people may be looking for contacts, co-founders, advice, etc, I think having a tool to get in touch with each other would be very useful. I vote yes do it, but KISS.
The person's website though would be something I would visit, and most people don't hide their websites on blogs.
EDIT: I should clarify: When a person writes a comment, it's the comment itself that would lead me to wonder what this person is all about. I'll click on his name. I'm not interested in a "profile", I'm expecting a website. The fact that I get the YC profile means I stop looking, and go back to reading the article. As such I never really figure out who the person is.
Many times I'd rather call someone up, but I may only have their email. Point is, there are usually always better alternatives. However, choices make the end goal more possible than it might have been.
The free text box in the profile lets the user give an email address, or their home page, or anything else including their phone number. The point is, they can limit how you can contact them. I don't think adding private messages on news.yc helps.
I a little more paranoid regarding privacy matters, but I am sure I'm not the only one.
A bit over a month ago i wrote a barebones PM util "addon" and submitted the link here. The feedback was generally good, while it was on the frontpage, then it whittled. http://news.ycombinator.com/item?id=18437
(it still exists, and I think still works, unless you changed the login mech).
As for stats, around 16 messages in the first 48 hours of the submission. Perhaps they were mostly test posts, but I did receive a few messages and an offer to trade email. Unfortunately he didn't check back when I sent him it :P
Just thought you'd know.
I am generally reluctant to email people directly for minor comments that I'd rather not post in public. I wind up just not communicating at all.
I also prefer to limit where my email address is posted online (obfuscated or not).
For serious things, email is generally worth it, but there still might be issues with spam filters or accidental deletions.