Which app do you use to count inventory? I prefer an app that allows you to scan the items' barcodes and enter a quantity or else to scan barcodes for each item and it totals the number of scans. If not that, have you found an app that allows uploading/entering quantities but more easily than through Products-->Inventory.
Using Airtable and then integrating/syncing Airtable with your Shopify store is one approach that works well. You have a spreadsheet interface to easily update/monitor inventory numbers, and you can use Airtable's phone app to scan barcodes. Check out our guide on how to manage and track Shopify inventory .
Even though I'm about 4 months late here, my company makes an app that does exactly this! Scan barcodes with your smartphone, count inventory while your store is open, have multiple people counting at once. We've spent a ton of time trying to make counting and managing inventory as easy as possible.
Check it out!