One of the things that came out of the Snowden files, I believe, was that ISP's will monitor someone that has a BitTorrent client (uTorrent, qbittorrent etc.) installed on their PC, even if they don't use it. It is possible to hide BitTorrent traffic using a VPN, but, hypothetically, how does one hide the very existence of a BitTorrent client on their computer from potential snoopers?
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Your bittorrent client isn't a service that they can go around scanning for, and ISPs certainly aren't going around hacking their customers computers (that I know of). Why doesn't downloading it with a VPN work or over HTTPS work? It's really impossible for an ISP to always tell what someone has on their computer. – Dec 09 '13 at 18:36
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Without a backdoor installed on your machine, an attacker would not be able to know what software was installed. If 100% of your traffic passes though an encrypted VPN, then it is not possible for an ISP to know what data is being transmitted. However, protecting the transport layer with a VPN may not conceal the type of protocol used to transmit the data. Researchers have claimed that it is possible to identify protocols protected by a VPN using statistical analysis, and other reservedness claimed that it is possible to identify encrypted BitTrorrent with information theory.
The only way for an ISP to know that a BitTorrent client was installed is by looking at the traffic it produces. If at any point the client calls home to check for an update, an observable condition has been created. Participating in the BitTorrent Distributed Hash Table, or visiting well known trackers is also a dead give away. But even if the data is encrypted, looking at a side-channel, such as comparing protocol timing signature, could reveal the use of a P2P protocol.
