Having the hide link right next to "N comments" makes it really easy to tap by accident. Then to unhide, you have to click through to your preferences to get to the "hidden" link.
Reddit uses this order:
N comments | share | save | hide | give award | report | crosspost
I guess my preference would be for HN to use a similar order:
N comments | N points by <user> <time> | hide | flag
Of course, if you make this change, half the readers will hate it and insist you change it back. :-)
I'm not sure that "flag" and "hide" need to be on the main page at all. You could show those only after clicking through to the submission?
(I should probably just switch to one of the many HN reader apps.)