@moco Seems like a good price. It looks to be a fairly compact enclosure. Will this be hidden inside your project?
I think you have to take a somewhat "disposable" approach to these projects. I have my system running completely off a large SDcard, and I have to live with the possibility (although I have not had an issue) that the card could get corrupted and require me to reformat. With safe shutdown etc. I should be able to avoid that, and you with your external drive may overcome that problem altogether, but as my project has evolved I have always considered all of the configuration, ROMs and artwork to be just the "working" versions in my arcade cabinet, knowing that I will eventually want to re-image. To that end, everything is stored in a network archive so I can rebuild if I need to.
I hope it works for you. If I do the HDD route, I might simply try to repurpose one of my bare 3.5" HDDs by adding a USB interface. The thing I like about thumb drives though is no noise, lower heat, and no moving parts to fail.