It's a problem and could be used to hide processes from the average sysadmin, but Bitcoin mining is not a likely use of this exploit.
Generally speaking, when virus writers write viruses, they don't like spinning up the CPU fans and literally allowing the user to hear the virus working. Pegging the CPU at 100% is the easiest damn way of getting caught.
Instead, Botnets seem to be more intent in stealing keyboard presses (credit card information, personal information), and launching DDOS attacks.
It's a ubuntu based subsystem. Apt-get probably uses their official repo and you would have to get your malware into that first and then make some windows beta-user install your new and unknown package.