The number of channels available on the RAID card does not automatically equal the number of drives.
On SATA-1, you need as many channels as you have drives, while SATA-2 lets you make use of hubs to expand in principle (but as total bandwidth is limited this slows things down, and it's not supported very widely).
If you're on SAS -- serial attached SCSI -- which can still let you use SATA drives (check out Near Line SAS, which is slower than SAS but gives you the scale of SATA, see http://www.techrepublic.com/blog/networking/how-sas-near-line-nl-sas-and-sata-disks-compare/5323), you can put up to 128 drives off a single HBA (host bus adaptor, the card you plug them into): http://www.attotech.com/support/trouble/sasfaq.html -- or up to 65,535 through expanders!
All that said -- if I were you I'd have a chat with the major vendors (say, Dell or IBM), and see what they have to say. That's some fairly expensive hardware...