On more formal bow-in's, some instructors will do a "clapping" which has origins from Shinto I believe. When the clapping bow in is done, I've seen students not participate. They will remain in seiza and only do the bowing... out of respect.
It is my understanding that the clapping action is a call to the spirits of the place, to pay homage to them, alert them to the coming practice and ask for their respect and pay respect for the practice that is taking place.
Students who do not follow those religious beliefs will just not take part. I've not seen anyone have a serious problem with it. I'm christian at heart, yet I will participate in the clap out of respect for the instructors that do this action. I'm still debating on the whole purpose and reason for the clapping, but I find no harm in doing it.
If God has a problem with me doing something, I think I would know. I have an instinct for things that are spiritual, and this is something that I'm still wrestling with... but at this time I just don't have a problem with it. Those that do have a problem with it should be respected and should not feel pressured to do something they are not comfortable with. Thankfully, this hasn't been a problem for anyone I've ever met.
That's my 2 cents.