To that end they teach to bow, but to not ever let your guard down while doing so. I'll give a bow to the sensei, to a fellow student before practicing a technique, and we have a ritualized closing ceremony of sorts. It's all designed to give structure to the learning environment. And it's a fairly ordinary Japanese thing to do as far as I can tell.
One of our young students' mothers was outraged that we bowed in class. She somehow has it in her mind we're worshiping Kano in some kind of shrine, which is not the point at all. She even offered to have her preacher contact me about how this was putting my immortal soul in peril. I know the preacher and he's one who, shall we say, likes to take liberties with Scripture to prove his point. No doubt he could lift a couple of familiar verses out and make a solid case as long as he's the one doing all the speaking. So now her son sits at home playing video games instead of learning a very useful skill, which I suppose is some kind of moral victory.
Some people just go around looking to be outraged. I prefer to go around learning new stuff from interesting people.