No, generally speaking it is not safe. Overclocking AGP above what video card can handle can only crash your system, but if your hard drive(s) aren't able to handle that speed, massive data loss/corruption could occur.
edit: Note that hard drive brand and model does matter, HDD controller crapping out is only a part of the equation. When bus mastering/DMA is enabled on a hard drive, the drive itself is responsible for at least some of the transactions.