Yes, the problem affects filesystem sync only 
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How early of a version of Joplin? The older versions which targeted older SDKs were allowed to access the filesystem more directly (= faster). The current versions are forced to use FUSE which is more secure but also very slow (e.g. see https://www.reddit.com/r/androiddev/comments/kpn68k/android_11_very_slow_file_access_performance). This is a known issue if you look up "android fuse" in any search engine. The only way to work around this would be through root, but Joplin doesn't have any special root mode which would allow for direct filesystem access.
When it comes to most other applications, users usually don't need to access hundreds or thousands of files at the same time, hence the problem is non-existent for them. However, with Joplin specifically, the application creases lots of tiny MD files for each note, and all together they can easily add up to a few thousands, and accessing such numbers of files on modern Android is very slow.