My experience is if it's on their website it can be ordered, but might be "pre-order". Most of the online dealers I've dealt with do not require any type of deposit. Of the online dealers I check The Train Shop, cttrains (McCormick's Hardware), and Legacy Station require a deposit. I don't typically buy much from them; they are just the online dealers I check.
To me, the bigger question is why don't some online dealers have items that are announced - MTH and Lionel - on their website? And sometimes it's listed, but I wait a while. When I check back later it's no longer listed. Wonder why.