The 3B+ truly just isn't powerful enough to handle that, I would highly recommend upgrading to a Pi4. This issue is decidedly less pronounced on a Pi4 but still present - though it takes an hour+ instead of minutes. The viewer software is still getting updated and support is still being provided for it, but not through the Keity brand. Link to the blog where updates are posted: https://blog-non-standard.blogspot.com/I recently got a RPi 3 B+ up and running with the 3DS Viewer software thanks to this post. (Thanks to RubyOtaku and WilliowTheWhisper!)
I do a have question though. There seems to be some pretty serious audio latency while using the viewer software. Upon startup of the Pi, the audio is synced, but over the course of about a minute, the audio becomes more and more laggy, until it's about a second behind the visuals. Is this normal behavior for the 3B+? Perhaps it's not powerful enough to run the viewer software without issues?