Strictly from a copyright perspective, I know of no impediment to the copyrightability of malicious code. In patent law, there is a requirement of an invention to possess "moral utility" -- that is, a utility that is not inherently morally abhorrent -- though no such requirement exists for copyright, not least because the question of "utility" is one that does not apply generally to creative works. If the work possesses a modicum of creativity and is original (or a derivative created with appropriate license), then it is covered under copyright. (However, as a fascinating tangent and mild counterpoint, have a look at the uneven history of the copyrightability of obscene works!)
However, your application might run afoul of other laws. For example, the distribution of software whose purpose is to circumvent access-restrictions to copyrighted works is a violation of the DMCA in the United States (in particular 17 USC § 1201(a)(2)). There may be statutes in some jurisdictions that similarly prohibit distribution of software that does some objectionable action (e.g., cooperation in a botnet). Your copyright and license on the malware may be legally valid, but you may be legally liable for violating a statute that prohibits distribution of malware.
I don't know to what degree you could be liable for malicious use of your botnet by another person, but it may be nonzero. (This will surely vary by jurisdiction.)