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Normally I would say software, or rather a raid-like filesystem like btrfs or ZFS. But in your specific case of funneleing it all through a single usb-c connection it is probably better to keep using an external box that handles it all internally.
That said, the CPU load of software raid it very small, so that isn't really something to be concerned with, but usb connections are quite unstable and not good for directly connecting drives in a raid.
I mean I've been running the setup this way for >4 years and never had any problem with the USB connection, so I cannot attest to "usb connections are quite unstable"...
I supposed that is because the JBOD box was handling the raid internally so short connection issues are not that problematic and can be recovered from automatically. But that wouldn't be the case if you connected everything together with a usb hub and usb to sata adapters and run a software raid on that.
I've been running a 4-disk RAIDz1 on USB for 4 years now with zero failures on one machine and one failure on another where it turned out the USB controller in one WD Elements was overheating. Adhering a small heatsink on it resolved the problem and it's been stable under load for 2 years now. The USB devices have to be decent. AMD's host controllers are okay. VIA hubs are okay. ASMedia USB-to-SATA are okay. I'm using some enclosures with ASMedia and some off-the-shelf WD Elements that also use ASMedia. It's likely easier to get a reliable system if installing disks internally as the PSU and interconnects are much more regulated and any would work well, whereas with USB you have to be careful in selecting decent components.