I've been through a similar scenario myself.
I had at one point put both name servers onto the same server and this worked fine. I used UKReg as the domain registrar and it had no problems the name servers being on the same IP address. Each name server should really be on a different IP Subnet for greater fault tolerance, one is hardly acting as a backup name server if it is on exactly the same machine. However, if you name server is on the same server as your web server, then all your eggs are in one basket anyway... my assumption is if your name server is on the same machine as your web server then if one goes down then the chances are they both have. Does that make sense?
On the other hand, I know there are good arguments for not doing this, ie, if your mail,sql server etc are on different machines then not all your services would go down as they would simply be directed from the backup name server.
I only have one IP address so had the same problem as you. The way I deal with this is use my own server as the primary name server and a free DNS service as the secondary name server. I use zoneedit.com which seems to work well.
Create an account with zone edit, tell it you want to use it's service as a backup/secondary name server service and give it the details of your primary name server and it's IP address.
Then go into ISPConfig DNS records and update the NS records, specifying the address of the secondary name server, mine is NS2.zoneedit.com. You must also give it the IP address that zoneedit supplied. Put the IP into the field marked 'allow export of records to IP address' (or very similar to that).
Remember to go and change the name server records with your domain registrar for the domains you wish to host so they know where to look.
I think that's pretty much how I did it.
It might be a nice idea for ISPConfig3 administrators who only have one IP each to team up and be NS slaves for each other.
Anyone feel free to comment my post if I've written incorrectly or my theory is wrong, I'm no expert, just passing experience.