If you're only using AVR boards then it shouldn't be a problem. It's only if you try to compile a program that uses the EEPROM library for a microcontroller of a different architecture that you'll encounter an error. The Arduino IDE automatically selects the EEPROM library associated with the hardware package of the board you're compiling for so each package can use its own version of the hardware-specific libraries (e.g: EEPROM, SoftwareSerial, SPI, Wire).
I'm glad I was able to help. Enjoy!
Per