It would certainly be courteous to inform users that logging for display on a public website is happening. That said, when I'm in an IRC channel I expect everyone is logging actively and I have no control over where those logs will end up. I guess I view it as speaking in public.
It'd be cool if irclogger would skip logging channels with +s/+p. Obviously it's up to the service runner which channels are added to the config, but it would let individual channels decide to opt-out (or even opt-out for a certain amount of time by setting/unsetting it.)