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You're thinking of trademarks. Different body of law.

EDIT: e.g. https://www.mozilla.org/en-US/foundation/trademarks/policy/

Logos can be part of both. A sufficiently unique logo (e.g. not just the name in Times New Roman) is absolutely copyrighted and an image of it cannot be distributed/reproduced without authorization unless fair use, which the malware project is not.

You're correct I was overly broad about the actual name use being DMCA-able though.

You can have copyright open source code, which is what allows open source licenses to enforce their terms. Open source doesn't mean "free to do whatever you want". There are very restrictive open source licenses, and you can deviate from the common open source licenses.

https://en.wikipedia.org/wiki/Software_copyright

Which project copyrighted its name and logo?

Logo? Every single one. All creative works automatically get copyright by default.

Now, projects might choose to license their logo permissively, but that's an active choice.