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, 


Depending on whether your site is a Modern or Classic site, you'll need to use the correct PowerShell script. They both use 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