I wouldn't worry about him, it's natural for new hamsters to act shy and scared at first. If he is only settling in he may be a bit nervous.
It is also possible that he has a hidden nest where he is going to the toilet. I've found with Bonnie, she only really poos in her nest or very close to the entrance of it, which is quite difficult to clean without disturbing her nest. But it's common for hamsters to 'go' in their nests as they spend a lot of their time there. (The plus side to this is that the rest of the enclosure stays pretty much clean.
)
Hope this helps x