is there any SOPC and NIOS2 design example of eeprom at93c46

If you open your sopc builder have a look at

Component Library -> Interface Protocols -> Serial -> SPI (3 Wire Serial)

just add and the configuration dialog opens.

Just set it to master, Data width 8 bit MSB first, Clock polarity 0 Clock Phase 0

assuming the added spi was named as spi_0, after generation you should get

Input MISO_to_the_spi_0 connect to AT93C46_DO

Output MOSI_from_the_spi_0 connect to AT93C46_DI

Output SCLK_from_the_spi_0 connect to AT93C46_SK

Output SS_n_from_the_spi_0 connect to AT93C46_CS via inverter

now you have connected the Atmel 93C46 to the SPI available via Nios SOPC