I have a SAM 440ep (OS 4.1u2, 2 TB SATA HD, onboard gfx) and have used dozens of various USB HD's, memory sticks, and a few networking items and never had a single issue with OS 4 not seeing said USB devices. I've never seen nor heard of requests from Poseidon/Trident a single time. Whatever OS 4.1 uses for USB handling, it's always does it completely transparently to me, I've never had a single issue with it. It's always run absolutely flawlessly with the above listed devices. Even when I plug USB sticks or HD's into my G 19 keyboard USB ports and such. After installing SAMBA, the SAM sees all the network shares on all my Windows boxes on my network just fine, which is handy.
I have not really had a reason to run many too MUI apps, but I am running MailManager (a legacy Fidonet mail tosser from the old days, a MUI app) on OS 4 with absolutely zero issues as well. As Redfox said, it comes with MUI. Not hit a problem yet with MUI apps.
Overall my summary on OS 4/SAM is: It's a fun little rig to have, but don't expect it to run all the old legacy apps well, and certainly don't expect it to replace a windows/mac/linux machine for internet purposes if you require modern browsers. Timberwolf isn't usable currently IMHO, but OWB works well. Some old apps still require emulation via UAE/GLUAE.
As a whole I am very happy with what I get out of my SAM and I enjoy it a lot, but as with all the new gen PPC Amiga's (or older legacy Amiga's with PPC/Bvision), the price can tend to be a little unjustifiable.