The experience is exactly the same when accessing the directly from the Files app. This makes sense because Affinity Photo for iPad relies on the Files app for file selection. The same is true for Lightroom Mobile. And Files still cannot open compressed RAF files. This reliance on Files for file browsing explains the lack of thumbnails, despite the fact that both Affinity Photo for iPad and Lightroom Mobile can open compressed RAF files.
The delay in even displaying a list of the files contained in a folder seems unrelated to file format. The Files app just seems to choke on a directory containing nearly 5000 images—and it appears that Files has no cache or indexing functionality that would make opening the same folder any faster the second time than the first. This is disappointing. FWIW, a folder of around 240 image files displays its contents almost immediately, whether they are compressed RAF or CR2.
The takeaway for Fuji shooters seems to be that Affinity Photo's new compatibility with compressed RAF files in v1.9 is less useful than it might seem. That said, there is a work around: Gnarbox. Gnarbox offers its own file browser which offers not just thumbnails but also large previews to aid in selecting the right image file. You still have to note the name of the image file and then open it using Open From Files in Affinity Photo but it is a far better solution than blindly opening image files without thumbnails until you find the one you want. The downside is that a Gnarbox, essentially a pocket-sized computer, can cost as much as an iPad.