If you've got so many USB devices that you're out of USB ports, I don't think you're concerned about cable clutter.
The only place I'm frequently out of USB ports is actually in front of the case. Most newer cases only have two ports in front, and for some odd reason manufacturers insist on dumping 5.25" (and 3.5") bays so you can't even add a few more. Its frequently not really ergonomic to use the rear ports too much.
Worse, they're usually placed so close together you can't even plug in a couple of outsized flashdrives-and-or-cardreaders in at the same time.
I know I've seen people talking about needing "at least 12 USB ports". I've got 4 cables coming out of my computer which sits under my desk. Power, HDMI, Ethernet, and 1 USB cable. Said USB cable runs to the top of my desk and my keyboard/mouse plug into it.
12 might be a little extreme. I have one for keyboard (which features an internal hub, so mouse is included), one for my monitors internal hub (doesn't see too much use since its behind the monitor), one for an external drive and one for an old (usually turned off) printer. So I'm good on pretty much anything.
Luckily my Crosshair features 2 USB3.1, 8 USB3 ports and 4 USB2 ports directly on the backplate. With headers for 5 more. So I'm well off...
In front of the case is a different matter. There are 3 (4 w/ dedicated charge port) ports from a hub (my case is so old it only features USB2 ports), and they're all frequently in use at the same time.