You can install additional drivers on the RoboRIO (provided it supports Linux) so software is generally not an issue. For USB, National Instruments does have a "durable" USB cable they were showing at St. Louis this year.
http://sine.ni.com/nips/cds/view/p/lang/en/nid/210962
Additionally, you could try using direct RS-232 or I2C with the arduino.