I can confirm that behavior.
Steps I reproduced the issue while I use the English test data:
1. I checked that the Module Banners is active in Extensions | Module Manager.
2. Extensions | Extensions Manager | Manage -> I disabled the Banner Module
3. Now the Module Banners is unpublished in Extensions | Module Manager.
4. I click on the red cross and I find the message “1 module successfully published”, although no Module was published. The Module Banners is still unpublished.

I had a quicker look at this issue and I think the main problem is, that it is possible to disable an extension also there is a published module. That’s why the editing view is OK. Only the module list is wrong.
I found a solution for this failure in the module list view. First I realized, that in
\joomla-cms\administrator\components\com_modules\models\modules.php
on line 240 the query measured the value for published. It combined the published value from modules with the enabled value from the extension table.

    $query->select(
        $this->getState(
            'list.select',
            'a.id, a.title, a.note, a.position, a.module, a.language,' .
                'a.checked_out, a.checked_out_time, **a.published+2*(e.enabled-1) as published,** a.access, a.ordering, a.publish_up, a.publish_down'
        )
    );

This leads to showing not the right values for published in this view.

I would suggest these changes in the file
\joomla-cms\administrator\components\com_modules\models\modules.php:

    $query->select(
        $this->getState(
            'list.select',
            'a.id, a.title, a.note, a.position, a.module, a.language,' .
                'a.checked_out, a.checked_out_time, **a.published as published, e.enabled as enabled,** a.access, a.ordering, a.publish_up, a.publish_down'
        )
    );

So the value for published is not changed and is consistent with the table, but we can use the enabled value of the extension table.

The second change is in the view file
\joomla-cms\administrator\components\com_modules\views\modules\tmpl\default.php

Here I would show Icons only, if the extension is enabled:

                    <td class="center">
                        <?php 
                        **if ($item->enabled>0)**
                        {
                            echo JHtml::_('grid.id', $i, $item->id); 
                        }
                        ?>
                    </td>
                    <td class="center">
                        <div class="btn-group">
                            <?php
                            **if ($item->enabled>0)**
                            {
                                echo JHtml::_('jgrid.published', $item->published, $i, 'modules.', $canChange, 'cb', $item->publish_up, $item->publish_down); 

                                // Create dropdown items
                                JHtml::_('actionsdropdown.duplicate', 'cb' . $i, 'modules');

                                $action = $trashed ? 'untrash' : 'trash';
                                JHtml::_('actionsdropdown.' . $action, 'cb' . $i, 'modules');

                                // Render dropdown list
                                echo JHtml::_('actionsdropdown.render', $this->escape($item->title));
                            }
                            ?>
                        </div>
                    </td>

So, in the module list view there would not show any icon. You can see an example in the attached file.

Is this a solution for this problem?

Should I open another issue for the problem, that it is possible to disable an extension, also there is a published module?

I am very new here. How can I attach this code to this issue?

attachement

Closing as we have a PR.