Realistically? No, they likely won't ban you for something that doesn't alter the gameplay or give you any advantage over your opponents.
Can they? Sure, technically it's modifying the client's files and against the ToS/EULA that we all agree to every time they update the game as well as when we signed up. It's their game and they're able to make the rules as they see fit, however they would much prefer you stick around and continue to play their game and/or spend money to enjoy yourself. The only problem they really have is if somebody is swapping around THEIR skins for the base models, thereby bypassing the system in place since someone put time (and Riot paid them real money) to make the skin.
I've been using custom skins for years and occasionally swap the UI's around (things like the Frost UI and Challenger UI that I'm sure you're able to find on the site that you found that one). Just make sure that it doesn't alter the way things are seen in the game (like changing positions of the target frame or making debuffs more visible - Riot if you're listening I would love to be able to move my target frame to somewhere not at the corner of my screen). It's an incredibly minor modification, and as long as the game's integrity isn't compromised there isn't really a reason for them to seek you out when there's much more pressing matters like ACTUAL cheaters (scripters, botters, etc.) that are ruining the game for others when you're a person looking to make your UI a little more immersive and continue playing as an honorable summoner.
Make sure you're not using programs that aren't already flagged as bannable as well as not using things like "zoom modifications" that would give you an unfair advantage. I'd recommend testing out any and all changes you do in a Custom Game/Practice Tool before hand to be able to ensure that nothing is changed in a drastic way as well as doesn't bug out! It's frustrating to queue up for a game while using your sweet Star Guardian Urgot skin (Rito pls, we need this) only to find out that you can't see the particles for when your E hit a target and you're scratching your head every time as to if it was accurate or not.
If they actually have a problem with it and it's not giving you an unfair advantage, they'll likely send you an e-mail to give you a "heads up" to remove it before any future problems happen.
Hope this helps, best of luck to you!