You need to use pagination, as detailed here: https://learn.microsoft.com/en-us/graph/paging
You can use this as example on how to do pagination via PowerShell:
$Apps = @()
$uri = "https://graph.microsoft.com/beta/applications?`$top=999"
do {
$result = Invoke-WebRequest -Method Get -Uri $uri -Headers $authHeader
$uri = ($result.Content | ConvertFrom-Json).'@odata.nextLink'
$Apps += ($result.Content | ConvertFrom-Json).Value
} while ($uri)