It sounds like your Archive reports have not processed all data, yet. Matomo recommends that you setup a cron job to process Matomo reports every hour for medium to high traffic sites. More information here: https://matomo.org/docs/setup-auto-archiving/
It is super weird today it started tracking again and I can see some “real”-time data. I really do not understand why this would happen because the browser showed the “tracking” requests but the server did not show them. I have multiple sites on this piwik installation and the others worked fine only this one had issues (I tested this this morning I forget to mention that yesterday).
Is there a way to see if the tracking requests have been “stored” or any kind of log that indicates the tracking requests that have been send to the server on the server side? It does not seem like Shopify is blocking those.
The traffic is not that heavy actually and it did not have any issues before.
Maybe you could try to invalidate the data of the days with corrupted data?
Also you can check the DNT setting. It is not possible (or very hard) to disable the DNT flag on Firefox for example, then in such case you won’t have traffic from any Firefox browser…