That mostly applies to 1v1 or small scale pvp. L2 is built around large fights (sieges, raids etc), where better tactics and numbers is what matters mostly, not rock-paper-scissors design, since you're supposed to have everything in order to be competitive anyway. Balance in L2 means that all classes are represented and can fill their role in large pvp.
For example, daggers' role (or rogue as you said) is to assassinate squishy key targets (healers mostly). In older chronicles ( T1> )he could not do that in mass pvps since he would immediately get focused by a mage/archer group or simply CC'd by some sws/bd/healer. Later he was given the tools to do his job (stealth/blinks) and started to rise in popularity at mass pvp.
Other classes are strictly outclassed by others. For example, EE > SE, WC > PP.
Others, like PS, have no purpose in pvp.
Others are represented in an unintended way. WK/ES were played as supports only before GoD. That was not what NC wanted when developing these classes.