Ok, I reproduced the issue on macOS High-Sierra and gdbm 1.15. Creating a DB creates a file of 16 MiB.

macbook:master haypo$ brew info gdbm
gdbm: stable 1.15 (bottled)
GNU database manager
https://www.gnu.org/software/gdbm/
/usr/local/Cellar/gdbm/1.15 (19 files, 569.8KB)
  Poured from bottle on 2018-06-19 at 13:48:35
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/gdbm.rb
==> Options
--with-libgdbm-compat
	Build libgdbm_compat, a compatibility layer which provides UNIX-like dbm and ndbm interfaces.

and

macbook:master haypo$ ./python.exe
Python 3.8.0a0 (heads/master:22525de, Jun 19 2018, 13:56:57) 
[Clang 9.1.0 (clang-902.0.39.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import dbm.gnu
>>> import os
>>> dbm.gnu.open("x", "c").close()
>>> os.path.getsize("x")
16777216