There are a couple questions burried in there, so lets get to it...
First, whether you buy a seperate domain name for each server, or use a subdomain like server1.yourcompany.com is only a choice that you can make. It's obviously more costly to buy a domain name for each box, and I doubt it accomplishes anything at all.
Not sure how #3 figures into this, but I'm going to guess what your question is.
You've got 12 servers. A client has his account on server #3. Which DNS servers are being used for his domain? Do they reside only on server #3? If this is the case, then it would make more sense to go a different route if possible.
You could arrange the servers in pairs or groups of 3 or 4. Lets say you do pairs. Server #1 and Server #2 would be setup with a DNS trust relationship whereby they BOTH have zone files (dns information) for domains on both servers. That gives you a little DNS redundancy which is always nice.
The other route, especially worth considering if you have more than one data center, would be to put another server up whose primary purpose will be as a master DNS server. It could maintain DNS zones for all 12 servers in the 'other' data center, and your clients might then use DNS servers like ns.yourcompany.com (the master server) and ns3.yourcompany.com (server #3's DNS). The advantage here is that you also gain redundancy of networks.
If this doesn't help, rephrase your question so we can help.