You can mix GPIB, USB, LAN. I use NI-VISA. I also use LabVIEW, but it just makes VISA calls, so as long as NI-VISA is installed (free download) I can send SCPI commands with LabVIEW, C, shell scripts, whatever.
GPIB cables are bulky. It's what I used for everything many years ago, but now it's mostly LAN. You just need a switch with enough ports for your gear. I'm not a fan of USB. As someone else said, seems more finicky. Hubs and enumeration and stuff. With LAN I set IP addresses to a dedicated subnet. For some reason someone at work settled on 172.9.33.x and I use that.
I would shy away from clone USB GPIB adapters. Google and you'll find all the time people put in getting things to work with this or that. I don't like the HP adapters either. The NI GPIB-USB-HS ones just work. You can get them off eBay used for <$200.
You're right, the SCPI commands aren't that complicated. You look up the commands you need from the manual, and just send them. Everything is sent and received as a string. For the reception you often have to parse the result to get what you want.