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One of sites (my oldest, largest, best known one naturally) seems to be a target of bots that scrape the content and republish it on random domains which then generate Google alerts back to me.

These random domains seem to be nothing more than scam sites to get the user to install malicious software and they never come up on actual Google searches.

Should I be worried about this somehow affecting my site placement? Or has Google gotten smart enough to know the difference between legit and non-legit content duplication (albeit not in the Google Alerts yet)?

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No.

It's an old question with different opinions, but usually there is no reason to invest energy dealing with such issues. It's especially true for already known websites with some reputation.

Read more about the basics of duplicate content issues.

And more relevant to you, if you do want to do something about it:

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