Their job postings have mentioned "next-gen" for quite a while now, which is why some people thought Skyrim won't come out until the next generation. So this really isn't anything new.
That's correct. Bethesda's HR probably just adds that tagline to every job posting they put out.
As for getting caught off guard by the 360, not likely. I am pretty sure they knew about it, but couldn't do anything about it until the actual API and specs were released by MS. The only people who know what's in the actual next-gen consoles, are the engineers working on them at this time.