How to generate a list of hidden items from list or document library list?

Avian 1 

Below script should give you all hidden lists / libraries in all sites

$SiteURL = "https://domain-admin.sharepoint.com/"
$UserName = "email address removed for privacy reasons"
$Password = "********"
$SecureStringPwd = $Password | ConvertTo-SecureString -AsPlainText -Force 
$Creds = New-Object System.Management.Automation.PSCredential -ArgumentList $UserName, $SecureStringPwd

Function Login {
    [cmdletbinding()]
    param([parameter(Mandatory = $true, ValueFromPipeline = $true)] $Creds)
    Write-Host "Connecting to Tenant Admin Site '$($SiteURL)'" 
    Connect-PnPOnline -Url $SiteURL -Credentials $creds
    Write-Host "Connection Successfull"
}

Function AllSiteCollAndSubWebs() {
    Login($Creds)
    $TenantSites = (Get-PnPTenantSite) | Select Title, Url       
       
    ForEach ( $TenantSite in $TenantSites) { 
        Connect-PnPOnline -Url $TenantSite.Url -Credentials $Creds
        Write-Host $TenantSite.Title $TenantSite.Url
        $subwebs = Get-PnPSubWebs -Recurse | Select Title, Url
        foreach ($subweb in $subwebs) { 
            Connect-PNPonline -Url $subweb.Url -Credentials $Creds
            $hiddenLists = Get-PnPList | Where {$_.Hidden -eq $true}
			foreach ($hiddenList in $hiddenLists) { 
				Write-Host $hiddenList.Title
			}
        }  
    }
}

AllSiteCollAndSubWebs

Hi Avian 1

Can you share your script to know it better?

Another thing - only lists and libraries can be made hidden and not list items. You can apply permissions on list items.