AFAIK SCSI controllers will not care how large harddrives you put on your machine, but IDE will. It's limited to 127 GB, but personally I'm running a 160 GB disk on my SCSI controller (CSPPC) without any problems.
Unless you got yourself an A4000T, you will need either an accelerator with SCSI controller or a Zorro SCSI controller in order to use your SCSI drives though.