The unstated hidden reason comments are disabled is because comment threads often dilute the message of the posting.
Threads can digress and accentuate negative, minor, or emotional/controversial distractions. The postings are a favor to the listing company. If that company prefers just "here's our message, contact us", with no risk of defocusing tangents, then that's the right favor for YC/PG to grant.
It may also be better to decide up front, "we'll give up the comments, good or bad", than to allow comments, and get a few that are so unproductively snarky they create a back-and-forth with critics, or that trigger premature speculation about things strategically left unsaid, or that prompt a later censorship decision (with its accompanying distracting gripetails).
Maybe ads are a type of content.
http://www.baekdal.com/publishing/why-traditional-ads-work-a...
The inevitable discussion about how we could just have an etiquette of not doing that, or a guideline for not doing that, or a new kind of flag button for that, or or or, will just serve to illustrate how much simpler a solution just not allowing comments on those posts is.
These posts aren't hurting you. My bet is most HN people actully think they're a benefit of HN --- early access to YC jobs! This is a fake controversy. Can we think about tolerating the YC job ads in terms of "least we can do for running HN"?
A posting anywhere with enough specific info to prompt applicant interest will prompt other observers to fill in the details. It's true for Google, Apple, Facebook etc. – so it will be true for self-identified YC startups who tout their impressive metrics as well.