Here's one possibility.  The command `\CommentInput{⟨file⟩}` reads the `⟨file⟩`, parsing it line by line, and rewriting the lines that start with a single `%` to a file `\jobname.cif` (cif stands for Comment Input File) without the leading `%`, then proceeds to read the `\jobname.cif` file back in.

I don't see how it would be possible to do this without the intermediate file while keeping the possibility of verbatim environments and commands with arguments spanning more than one line.  But I think the extra file shouldn't be that big of an issue.

The code takes care to make a file substitution so that file hooks still work by name on the original file you want to read in, rather than on the temporary file.

This behaves different from `\DocInput` regarding the `%` sign:  `\DocInput` makes a `%` catcode-9, so it's completely ignored (anywhere in the line) while here only the first `%` is removed and the other ones are still comment characters (also `^^A` is not a comment char then).  This is harder to change because then unless the `doc` package is loaded, the `verbatim` environment will see the should-be-ignored start-of-line `%` character and will typeset it.  It is easy to change though, if you intend to use this with `doc` and prefer the all-`%`-are-ignored behaviour.

And without further ado, here's the code:
```
\documentclass{article}

\begin{filecontents*}[overwrite]{duck.sty}

\newcommand{\quack}{Quack!}

% line to be included in the other document
% \begin{verbatim}
% something verbatim to be included in other document
% \end{verbatim}

%% line not to be included 

\end{filecontents*}

\ExplSyntaxOn
\makeatletter
\iow_new:N \l__samcarter_iow
\tl_new:N \l__samcarter_file_name_tl
\NewDocumentCommand \CommentInput { m }
  { \samcarter_comment_input:n {#1} }
\cs_new_protected:Npn \samcarter_comment_input:n #1
  {
    \file_get_full_name:nNTF {#1} \l__samcarter_file_name_tl
      { \__samcarter_comment_input: }
      { \msg_error:nnn { samcarter } { file-not-found } {#1} }
  }
\msg_new:nnn { samcarter } { file-not-found } { File~'#1'~not~found. }
\cs_new_protected:Npn \__samcarter_comment_input:
  {
    \group_begin:
      \cctab_select:N \c_other_cctab
      \int_set:Nn \tex_endlinechar:D { `\^^M }
      \use:x { \tex_everyeof:D { \exp_not:N \q_nil \char_generate:nn { 13 } { 13 } } }
      \char_set_active_eq:NN \^^M \__samcarter_process_line:w
      \char_set_catcode_active:N \^^M
      \iow_open:Nn \l__samcarter_iow { \c_sys_jobname_str . cif } % cif => comment input file
      \exp_after:wN \__samcarter_process_line:w
        \tex_input:D { \l__samcarter_file_name_tl }
      \iow_close:N \l__samcarter_iow
    \group_end:
    \declare@file@substitution { \l__samcarter_file_name_tl } { \c_sys_jobname_str . cif }
    \input { \l__samcarter_file_name_tl }
    \undeclare@file@substitution { \l__samcarter_file_name_tl }
  }
\group_begin:
\char_set_catcode_active:N \^^M
\char_set_active_eq:NN \^^M \scan_stop:
\cs_new_protected:Npx \__samcarter_process_line:w #1 ^^M
  { \exp_not:N \__samcarter_parse_line:w ^^M #1 ^^M \c_percent_str \s_stop }
\cs_set_protected:Npn \__samcarter_tmp:w #1
  {
    \cs_new_protected:Npn \__samcarter_parse_line:w ##1 ^^M #1 ##2 \s_stop
      {
        \tl_if_empty:nTF {##1}
          {
            \peek_charcode_remove:NTF #1
              { \__samcarter_ignore_line:w }
              { \__samcarter_output_line:w }
            ##2 \s_stop ^^M
          }
          {
            \tl_set:Nx \l_tmpa_tl { \tl_tail:n {##1} }
            \tl_if_eq:NNF \l_tmpa_tl \q_nil { ^^M }
          }
      }
    \cs_new_protected:Npn \__samcarter_output_line:w ##1 ^^M #1 \s_stop
      { \iow_now:Nn \l__samcarter_iow {##1} }
    \cs_new_protected:Npn \__samcarter_ignore_line:w ##1 \s_stop { }
  }
\exp_args:No \__samcarter_tmp:w { \c_percent_str }
\group_end:
\makeatother
\ExplSyntaxOff

\begin{document}

some text

\AddToHook{file/before/duck.sty}{A line added with a hook\par}

\CommentInput{duck.sty}

\end{document}
```