I tried to find a source for these concerns. Although I can find documentation on DDC (until 1998) and EDDC (since 1999), and indeed read that these often use EEPROM, I cannot find any reference of someone who broke his monitor by changing the brightness too often.
This utility is very useful combined with the adaptive brightness of my iMac so I am tempted to use it. But I would appreciate any supporting evidence of this concern.