Ignore the answer on AD, as yours is about Domino. As for putting servers under an OU, that is fine. I generally create an OU just for servers, like /Servers/Domain Name so that I can put the wild card entry of */Servers/Domain Name into ACLs and the like for ease of administration.
Each domain controller in an Active Directory forest can create a little bit less than 2.15 billion objects during its lifetime.
Hope the is link will help