Nearly. You don't need Sync mode*, just Phase Init. But yes, two square waves (or sine, or triangle) at identical tuning will cancel each other out when a phase init of 64 (180°) is used for Osc 2.
Try it yourself.
• Load up the patch called -START- or -INIT-
• then change the Osc Balance knob to zero (the middle) so you can hear both oscillators.
• turn Osc 2 detune down to zero.
• change both Osc 1 and Osc 2 to Pulse waveform
• set Phase Init of Osc 2 to be 64.
Press a note, and you should be able to hear.. not a lot really. You might hear a click or pop as you hit a key but this is due to the Punch Intensity. You can turn Punch down to zero in the main edit menus.
You might hear it slowly phasing slightly but this would be due to fine detune values of Osc 2, or the analogue-esque emulation side of the Virus (subtle detune instabilities - if you want clinical waveform accuracy, turn up PureTuning to the max).
* Sync mode is a completely different function to Phase Init.
Phase Init merely starts Osc2 at a particular phase position - the oscillator is free to do whatever it wants thereafter, it's free running.
Sync mode, however, forcefully resets the phase of Osc2 to 0° everytime Osc1 completes its own phase cycle.
Graphic illustration of sync mode:
http://www.infekted.org/virus/files/sync.png