tools: prefer filter to remove empty strings

Ref: https://github.com/nodejs/node/pull/23585#issuecomment-430585490

Python's `list.remove` will throw if the element is not found and also
it removes only the first occurrence.

This patch replaces the use of `list.remove` with a `filter` which
solves both of the above mentioned problems.

PR-URL: https://github.com/nodejs/node/pull/23727


Reviewed-By: Richard Lau <riclau@uk.ibm.com>
Reviewed-By: Luigi Pinca <luigipinca@gmail.com>
Reviewed-By: Rod Vagg <rod@vagg.org>
Reviewed-By: Refael Ackermann <refack@gmail.com>
Reviewed-By: Matheus Marchini <mat@mmarchini.me>
Reviewed-By: Colin Ihrig <cjihrig@gmail.com>
Reviewed-By: James M Snell <jasnell@gmail.com>