The Peter Cederqvist manual recommended the practice.
Here is a 1993 dated copy someone left hosted:
https://www.astro.princeton.edu/~rhl/cvs/cvs.html
The paragraph which recommends the .keepme files is:
https://www.astro.princeton.edu/~rhl/cvs/cvs.html#SEC63
"if you want an empty directory then put a dummy file (for example `.keepme') in it to prevent `-P' from removing it."