For most of my work I deal with screen printing prepress. In the end, it's all the same to me. Regardless of how clean the swatch panel might look, my workflow will remain unchanged. In fact, I'm pretty much going to ignore the provided swatch panel and create my own. So to answer your best practice question: I don't care what you do. It's not that I enjoy duplicating work that's already been done, it's that I don't trust other designers!
I see artwork from all ranges of expertise, anything from a hand-sketched logo pasted into a Word document to corporate artwork with the accompanying branding guide. It's a sigh of relief when I'm given well organized artwork that is easy for me to work with, but I will never assume that it's flawless. I'm still going to double check that there isn't a fifth spot color hiding in the artwork if they're asking for a four color print.
Despite that, your efforts are not done in vain. When I do come across an issue with the artwork, that's potentially adds more communication back and forth about pointing out the issue and suggesting how it should be solved. Adding this step to your workflow can help eliminate oversights.
Seeing well-crafted artwork also builds respect, and that can certainly go a long way when it comes to establishing a good relationship with your printer.