You may have to install the font of your choice on the linux machine. Once it is installed, you can specify the font for a control, indicator, etc. by using the 'text settings' option in the tool bar.
Using VI Server, you might be able to do a mass change of the fonts for labels and captions. The following webpage contains an example that changes the value of controls -- you could modify this example to modify the fonts:
http://zone.ni.com/devzone/explprog.nsf/6c163603265406328625682a006ed37d/56685792886a556e86256740007fe32a?OpenDocument
I did not thoroughly test this so this option might not be 100% snag free....