The Navo sites page currently only displays top-level sites and site collections in SharePoint Online. In order to add Navo to a site that's not displayed, you can either click on the Can't find your site? option or use PowerShell, The below code will add Navo to any site you target it at. It uses Microsoft's PnP SharePoint Module for PowerShell, which you'll need to download first.


Modern Sites:

Connect-PnPOnline -Url "URL HERE"
Add-PnPCustomAction -ClientSideComponentId 27b0cb87-695b-4405-ae63-9db7d67e1029 -Location ClientSideExtension.ApplicationCustomizer -Name s-masthead-spx -Title Masthead 


Classic Sites:

$siteUrl = "TARGET SITE URL"
$appCatalogUrl = "APP CATALOG URL"
$script = @"
(
function () {
var appCatalogSiteUrl = "$appCatalogUrl";
var mastheadListName = "DO_NOT_DELETE_MASTHEAD_LIST";
var classicListItemTitle = "classic-list-url";
(function () {
var request = new XMLHttpRequest();
request.open("GET", appCatalogSiteUrl + "/_api/lists/getbytitle('" + mastheadListName + "')/items?`$filter=Title eq '" + classicListItemTitle + "'&`$Select=Url,Title", true);
request.onreadystatechange = function () {
if (request.readyState === 4 && request.status === 200) {
var json = JSON.parse(request.response);
if (!json.value[0]) {
return;
}
var script = document.createElement("script");
script.type = "text/javascript";
script.src = json.value[0].Url;
document.getElementsByTagName("body")[0].appendChild(script);
}
};
request.withCredentials = true;
request.setRequestHeader("Accept", "application/json");
request.send();
})();
})();
"@

Connect-PnPOnline -Url $siteUrl
Add-PnPJavaScriptBlock -Name "Masthead Classic" -Sequence 8448 -script $script