It is entirely up to you. rclone is very flexible here - you can encrypt content but not names, only names or both. personally I do not see reason not to use full encryption (both content and names). It is only mode which provides full privacy.
First question should be what you want from encryption? what you try to hide? and from whom? People do all sort of things and have different requirements. I would never leave not encrypted files names. Because I do not like cloud provider to see what I store - as a matter of principle:) But you might have different attitude - and it is perfectly ok.