Periodical editors have given me a whole range of opinions on this, from "that's a great letter, send it" to what you've said above. I remain confuzzled about what the right thing to do is - but I do think, if the magazine's posted guidelines say three months, and after six months I send a letter asking about my ms's status, and there's no reply, and then the one year mark goes by, then I need to be able to withdraw the material. I thought giving them an extra 60 days was nicer than pulling it immediately, on the off chance they were considering it.

This has happened to me four times (out of literally thousands of submissions, so it's not like it's common) and two of those times, the editor emailed me and asked me to resubmit. The other times I got no reply at all (one of those magazines turned out to have gone out of business; never did find out what happened with the other one, maybe I pissed them off).

I guess the difference between unsolicited novel submissions and unsolicited periodical submissions is that you can, presumably, submit your partial elsewhere while you're waiting for a request for the full (can't you? I've never submitted a novel), whereas I can't submit my poem/short story elsewhere until I hear back from them.