Didn't say it wasn't a pain. I usually explain to the client it's a bug. I get over it. Nuendo has always been a little dicey when using mutes/ solo and automation. As long as when I mix the shit works (which it does) I swear and move on.
Long ago I started using the mute tool in the proj window for about 1/2 my mutes and I make a habit of using disable on the tracks that I know are out of the picture. The majority of my mute automation is for delay returns. Also muting edit groups with the mute tool is much faster when muting multiple tracks. I'd still do it that way if I was mixing on a SSL. Faster and cleaner.
Don't get me wrong, I want a flawless DAW but I'm willing to work with what I have as long as it makes the process better not worse.
Every user has some gripes with their DAW. I hear PT users ragging all the time about this and that but they still use PT.
Nuendo may not be perfect though it's still killer.