Personally I'd make an array, pull your user list, and then iterate through the secondary SMTP addresses for each user adding your custom object to the array for each entry.
$Userlist = @()
$searchBase = 'OU=Users,DC=Contoso,DC=LOCAL'
$users = Get-ADUser -filter 'enabled -eq $true' -SearchBase $searchBase -Properties DisplayName
Foreach ($user in $users){
$Recip = get-recipient -Identity $user.samaccountname -ErrorAction SilentlyContinue| select Name -ExpandProperty emailaddresses |? {$_.Prefix -like "SMTP"}
$Recip|? {$_.IsPrimaryAddress -like "False"} |select -ExpandProperty Smtpaddress |%{
$UserList += New-Object -TypeName PSCustomObject -Property @{
Name = $User.DisplayName
"Login ID" = $User.SamAccountName
Primary = $Recip|? {$_.IsPrimaryAddress -like "True"} |select -ExpandProperty Smtpaddress
Secondary = $_
}
}
}
This script (based off your script above) also reduces the number of server queries by 3 per user I think, so it should run a ton faster.