Do APPS like these interfere in any way with OS X?
I'm not sure what you're getting at. I'm not sure I'd call changing an icon "interference". I've customized folder icons, as well as some app icons since I've been using OS X (Mountain Lion - Yosemite) and never suffered any ill effects. You used to be able to do it quite easily using Finder alone. If it makes you feel better, the app
Folder Designer is distributed through the Mac App Store, which means its been fully vetted by Apple, adhering to all sandboxing requirements. While not allowed on iOS, Apple's been selling OS X icon changer apps for years.