I’ve had nothing but problems with SSD enclosures in general. I tried just having an SSD as a portable game drive and was basically facing the same issue you were. But I don’t think it’s Steam Deck specific, the same issue was happening on my PC.
I think part of it is the power supply needed for the SSD drawing higher than the hubs like? Direct connect on PC mostly no issues, via hub it has drops. Haven’t direct connected to Steam Deck but it seems to have the same issue with the SSD staying connected to the hub.
I was using an ASUS enclosure. Narrowed one issue down to a USB cable itself but even still that didn’t solve the same long term issue, which it seems you’re running into as well.
I’ve noticed the same behavior but I’m not sure it’s explicitly Deck specific, it may legitimately be a USB protocol thing preventing this or something.