Get all metafields for products

I have many products (100 000 for example). But Shopify doesn’t allow to store SKU (why?!?!?!?!?!?!?!?!?!?!) and as result I must store SKU inside metafields and any time I must fetch metafields for any products to check if product available in shop or not. Now I have API calls = products pages count + products count just to read available data. If I have 100 000 products - I must use more than 100 000 calls because I can’t use pagination with next parameters:

/admin/metafields.json?metafield[key]=SKU&metafield[owner_resource]=product

Now API have limits: 2 requests per second.

100 000 products / 2 requests / 60 seconds / 60 minutes = 14 HOURS!

During this time my product list can be changed many times.