Depending on your Server, disk space meight not be the first thing you are running out off.
Depending on what scripts your customers run, CPU and RAM can become a bottle neck. Just consider 5000 typo3 installs and a decent amount of traffic to all of them.
... gladly that won't happen over night, and you will probably have time to extend your ISPConfig installation to a multi-server setup, so you can create new customers on seperate machines, all managed from one interface.
As for your disk szenario, you can prepare for this situation beforehand by using LVM for your / partition. That way, when you run out of diskspace, you slide in another HDD, add that physical volume to your exisiting volume group extend your logical volume, grow the filesystem and everything is fine. If your system is hotswap-able (most SATA controllers are nowadays), all of that can be done without any interruption of service aka online-resize.