A standard emerged in websites many years back:
* logo in in the upper left (which is also a link to the home page)
* search is a text box in the upper right.
If you're not doing it this way, you're imposing an unnecessary cognitive load on your users.
It's kinda part of the fun, and if you stick around long enough, you 'discover' (aka level up) little things about HN that increases your skill level at using HN.
Without an easily accessible link, it's difficult to search content on the site. I've been a member for a long time, and I didn't know that searchYC existed until reading this post (previously I had been using Google, which isn't so great at indexing HN).
git clone git@github.com:zacharydanger/greasemonkey-searchyc.git
for a peak at a search box that hits searchyc.comDeleted comment
As for search, even though it's another step, searchyc.com does a good enough job. maybe all pg needs is a form with an api to searchyc.
cooper@ubuntu:~/arc3$ grep -r -i search *
strings.arc:; http://jrgraphix.net/research/unicode_blocks.php?block=1
cooper@ubuntu:~/arc3$ du -sh .
312K .
cooper@ubuntu:~/arc3$Personally, it's the current content of HN that interests me first and foremost (the NEW in NEWS). Putting the searchbox in the footer would emphasise this and not break the site design.