Office 365 licensing and reporting

Yes, the reports definitely have some room for improvement, as Tony described recently here: https://www.petri.com/get-mailboxstatistics-cmdlet-wrong

If it's only Exchange data you care about, you can look at the message trace logs and check when was the last time a user send (or even received) a message. You can also enable mailbox auditing and check for "owner" actions. And you should be using the standalone Exchange plan 1/2 licenses in this scenario, as they are much cheaper compared to the "package" ones.

The situation is not that different for other workloads too, data in the reports is often missing or incorrect, so you might have to rely on checking the Audit logs instead (which are also prone to some issues). But if you augment the report data with data from other sources such as the Audit logs, you will get a better picture overall.