In general, “bad practice” is so common in the wordpress ecosystem, you will have to do something really bad for anyone to actually signal you out for doing it 😉
If you are the developer and maintainer of the theme, you should develop it in a way which will be easy for you to maintain in the long run, regardless of what other people’s preferences are.
If someone else is going to maintain it, keep as much as you can to the structures used by the core themes. That said, in this specific case, even if they don’t do it this way, it looks easy enough to understand by anyone that had ever worked with wordpress themes.