Updated August 05, 2019 to fix an error when used on the root site and the BaseUrl field was set to /. To load the lists on the root site you must leave the field empty.

Here is a tool to toggle the visibility of all custom lists (BaseTemplate 100) and document libraries (BaseTemplate 101) – and also the Site Pages library (BaseTemplate 119). It is used to toggle the Hidden property on the list – which determines whether or not to show the list in Site Contents.

Please note that you must have the necessary rights (manage lists) to use it, and if you don’t you will get an error message. Also note that this snippet loads jQuery from code.jquery.com – if your site does not have Internet access you must change this script tag to refer a local copy of jQuery.

Add this snippet to a Script Editor Web Part in a Classic Web Part Page to use it.

<div class="pageHeader">BaseUrl to the site</div>
<input type="text" style="width:200px;" id="baseUrlInput" onkeydown="if(event.keyCode === 13){getAllLists()}"><input
    type="button" onclick="getAllLists()" value="Load all lists" />
<div id="allListsTable"></div>
<style type="text/css">
    .pageHeader {
        font-size: 1.5em;
        font-weight: 300;
    }

    .headerRow td {
        font-size: 1.5em;
        border-bottom: 1px silver solid;
    }

    .bodyRow td {
        padding: 3px 5px;
    }

    .bodyRow:hover td {
        background-color: #00ad56;
        color: #ffffff;
    }
</style>
<script src="https://code.jquery.com/jquery-3.4.1.min.js"
    integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<script type="text/javascript">
    jQuery("#baseUrlInput").val(_spPageContextInfo.webServerRelativeUrl !== "/" ? _spPageContextInfo.webServerRelativeUrl : "");
    function getAllLists() {
        var baseUrl = jQuery("#baseUrlInput").val();
        jQuery.ajax({
            "url": baseUrl + "/_api/web/lists?$select=Id,Title,BaseTemplate,RootFolder,Hidden&$expand=RootFolder",
            "method": "GET",
            "headers": {
                "accept": "application/json; odata=verbose",
                "content-type": "application/json;odata=verbose",
                "X-RequestDigest": getFormDigest()
            },
            "success": function (data) {
                var arr = [], b = [];
                jQuery.each(data.d.results, function (i, list) {
                    if (list.BaseTemplate !== 100 && list.BaseTemplate !== 101 && list.BaseTemplate !== 119) {
                        return;
                    }
                    arr.push({
                        "title": list.Title,
                        "rootfolder": list.RootFolder !== undefined ? list.RootFolder.Name : "",
                        "id": list.Id,
                        "hidden": list.Hidden
                    });
                });
                arr.sort(function (a, b) {
                    if (a.title < b.title) {
                        return -1;
                    }
                    if (a.title > b.title) {
                        return 1;
                    }
                    return 0;
                });
                b.push("<table>");
                b.push("<tr class='headerRow'>");
                b.push("<td>");
                b.push("Title");
                b.push("</td>");
                b.push("<td>");
                b.push("URL-name");
                b.push("</td>");
                b.push("<td>");
                b.push("Hidden");
                b.push("</td>");
                b.push("</tr>");
                jQuery.each(arr, function (i, list) {
                    if (list.rootfolder === "") {
                        return;
                    }
                    b.push("<tr class='bodyRow'>");
                    b.push("<td>");
                    b.push(list.title);
                    b.push("</td>");
                    b.push("<td>");
                    b.push(list.rootfolder);
                    b.push("</td>");
                    b.push("<td>");
                    b.push("<input listguid='" + list.id + "' type='checkbox'" + (list.hidden ? " checked='checked'" : "") + " onclick='toggleVisible(this);'/>");
                    b.push("</td>");
                    b.push("</tr>");
                });
                b.push("</table>");
                jQuery("#allListsTable").html(b.join(""));
            },
            "error": function (err) {
                jQuery("#allListsTable").html(err.statusText + ": " + err.status);
            }
        });
    }

    function toggleVisible(elm) {
        var baseUrl = jQuery("#baseUrlInput").val();
        var hidden = jQuery(elm).prop("checked");
        var guid = jQuery(elm).attr("listguid");
        jQuery("#status_" + guid).remove();
        var itemPayload = {
            "__metadata": { "type": "SP.List" },
            "Hidden": hidden,
        };
        jQuery.ajax({
            "url": baseUrl + "/_api/Web/Lists/GetById('" + guid + "')",
            "type": "POST",
            "data": JSON.stringify(itemPayload),
            "headers": {
                "accept": "application/json; odata=verbose",
                "content-type": "application/json;odata=verbose",
                "IF-MATCH": "*",
                "X-HTTP-Method": "MERGE",
                "X-RequestDigest": getFormDigest()
            },
            success: function (data) {
                // Success
                jQuery(elm).after("<span id='status_" + guid + "' style='margin-left:4px;'>OK</span>");
            },
            error: function (err) {
                jQuery(elm).after("<span id='status_" + guid + "' style='margin-left:4px;color:red;'>Error! - Open the console for details (F12 > Console).</span>");
                console.log(err);
            }
        });
    }

    function getFormDigest() {
        var r = _spPageContextInfo.formDigestValue;
        if (r === undefined) {
            r = jQuery("#__REQUESTDIGEST").val();
        }
        return r;
    }
</script> 

Hope you find this tool useful.

Alexander