Typically Riot can't tell if you were the one who installed them or not. I am not saying you are lying, but it would be very unlikely that someone didn't know that they installed a third-party modification to League of Legends.
Why don't you get a warning when you install it? Because you have to physically install the mod on your computer, Riot assumes you would know it's there. Also, if they warned everyone running third-party mods, it would give information to the people who make them, which they can use to get around Riot's security that they have built into League of Legends to prevent people from modifying it.
If you want to contest it and have Riot look into your account, you can always send them a support ticket. Be respectful, to the point, and clear if you send the ticket. However, third-party modification of any kind is strictly forbidden in the Terms of Use, so don't be too surprised if they don't reverse the ban.