The JTAG UART data rate depends on how you put data through it. On standard USB-Blaster it can get up to about 1Mbit/s if you send enough data to keep it busy.You have to have code on the target which services it quickly enough though especially on host->target transfer. If the target can't keep up then the host slows to a crawl because of the number of retransmits it has to do.
Please use the general Nios II forum for questions like these. This is the C-to-Hardware accelerator section. Moving this and the other threads that don't belong here over.