How destructive is Automatic Click Remover?

Clicks have (fortunately, or it wouldn't work at all) a sonic signature that's quite distinctive, and this is relatively easy to detect. They  are also pretty unlike any form of musical sound, either in their shape or duration. This means that within reason, you won't have a problem with what's extracted. You might though have a problem with what isn't, though, as anything larger than yer average 'click' won't get fixed.

Personally I wouldn't use the Automatic Click Remover. I'd far rather use the Click/Pop Eliminator - the process-based one. You get far more control, and generally much better results. Also if you're de-clicking records, you'll find that not all clicks are equal, and there's one trick that can often help a lot. Convert your stereo to a Mid/Side (there's a preset in the Channel Mixer), and you'll find generally that there are far more clicks in the Side channel than the Mid. So you can treat them separately, to some advantage. When you're done, convert back to normal stereo, and you should get a result that's technically better, and may even sound better!