If you don't plan on moving the computer around it would be fine. Not a bad idea either. The ATA bus that has the usual Zip and DVD drive is a second bus. Take out the zip drive and you could install a second ATA drive without a card. I don't use zips much anymore and I do have a G4 with a zip drive so this would be an option for me as well.
Basically any hard drive needs airflow around it...if you can find a way to mount it in the zip carriage that would be fine.
If I was to buy a PCI card, I would suggest getting two ATA drives and stripe them into a RAID...much better performance and twice the storage.