Files ending with "~" are treated as hidden files, when in fact they are often 'backup' files; "~" is a common backup suffix. However, 'hidden' and 'backup' are not equivocal, and treating them as such is confusing and potentially dangerous. An experienced linux user is familiar with what normally constitutes 'hidden' - i.e. something that begins with '.' - something that is listed with `ls -a` but not with `ls`.
Example of 'dangerous' screnario:
You move / remove a file with sensitive content from an insecure location in that filesystem, but unbeknownst to you a backup copy is still lingering there!!
I understand that the current behaviour mimics other file managers - that doesn't necessarily mean it is correct. I suggest that you make 'hidden file types' configurable through preferences. 'Hidden' files could include '.' files, and optionally files that match user-defined suffixes or prefixes. You could easily include the "*~" suffix by default to maintain the current default behaviour, but giving advanced users the freedom to change this is desired.
Thanks for your time.