For the purposes of getting an idea of user count, I would suggest summing the user counts for both Jira applications. It's possible (and even likely) that some Jira Service Desk users are also licensed for Jira Software - for user count purposes a person in both applications might count as one user. But for billing purposes, that's two licenses.
We don't currently have a hard limit on storage - from the document you've linked:
If your Atlassian Cloud instance exceeds the storage limit, your instance will not be suspended, except in extreme circumstances, and we will not remove any data. If you exceed your storage limit by a small amount, and you're storing acceptable types of data, your products will continue to work (large video files are an example of an unacceptable attachment data type). If you exceed the limit by a large amount, we'll email your technical contact and offer help to reduce disk usage by archiving old Confluence or Jira product attachments.
It's also not possible at the moment to get an estimate of what your storage usage is from site administration. We have a few feature requests around this - I'd recommend watching and voting on CLOUD-2770 to stay informed on the happenings in this area.
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