I've not had any issues over the last year and a half running the VST/ASIO method other than turn off pop. I fixed that with a PAC TR-7. Now this is not to say something else might not go horribly wrong. If I shutdown Console, then there is no software route for the sound to get to the hardware. This might purely depend on hardware and how stable the soundcard drivers or 3rd party audio stream routing is done.
Ways to protect your speakers (and maybe your hearing):
1) Kill switch on amp remote turn on wires for instant off in case of "problems"
2) Analog volume control inserted between computer and amp(s)
3) Capacitors inline on tweeters to protect them (6dB high pass filter). Pick a high frequency below your filter frequency as to not affect it but still offer protection from frequencies that could damage tweeters from overexcursion.
As for square waves: this can affect any speakers. The only way to possibly protect against that is probably a properly sized light bulb that acts as a protection fuse. I have never seen a computer output square waves if they freeze-stutter yes (but that is not a square wave), does this mean it can't happen? I don't have an answer for that, but I would sure hope GOOD soundcard manufactureres worry about such problems for you.
There is a
huge long thread over on DIYA on using the PC as a home based XO. I'm quite sure this topic had to have been brought up considering some of those guys could be running speakers costing well into the thousands upon thousands of dollars.